@article {pmid39266450,
year = {2024},
author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C},
title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {Supplement_1},
pages = {},
doi = {10.1093/bib/bbae429},
pmid = {39266450},
issn = {1477-4054},
support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; },
mesh = {*Biofilms/growth & development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; },
abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.},
}
@article {pmid39264803,
year = {2024},
author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L},
title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387402},
doi = {10.1080/19490976.2024.2387402},
pmid = {39264803},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation & purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; },
abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.},
}
@article {pmid39264513,
year = {2024},
author = {Angebault, C and Botterel, F},
title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.},
journal = {Mycopathologia},
volume = {189},
number = {5},
pages = {82},
pmid = {39264513},
issn = {1573-0832},
mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Microbiota ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.},
}
@article {pmid39259188,
year = {2024},
author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A},
title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae169},
pmid = {39259188},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestAntibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.},
}
@article {pmid39197244,
year = {2025},
author = {Zhang, C and Gu, C and Wang, M and Chen, J and Chang, H and Chang, Z and Zhou, J and Yue, M and Zhang, W and Zhang, Q and Feng, Z},
title = {Effect of temperature regulation on microbial community, volatile flavours, amino acid profiles, and iridoid glycosides during noni (Morinda citrifolia L.) fruit fermentation.},
journal = {Food chemistry},
volume = {462},
number = {},
pages = {140966},
doi = {10.1016/j.foodchem.2024.140966},
pmid = {39197244},
issn = {1873-7072},
mesh = {*Fermentation ; *Fruit/chemistry/metabolism/microbiology ; *Amino Acids/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; *Morinda/chemistry/metabolism ; *Iridoid Glycosides/metabolism/analysis/chemistry ; *Temperature ; Volatile Organic Compounds/metabolism/chemistry ; Flavoring Agents/metabolism/chemistry ; },
abstract = {Noni fruit has an unpleasant flavour but is highly bioactive. Therefore, it is necessary to clarify the effect of temperature regulation on quality of fermented noni fruit. In the present study, the formation of flavours, amino acid profiles, and iridoid glycosides during noni fruit fermentation at different temperatures were investigated. We initially found that different temperatures affected core microbial communities. The general evolutionary trends of Acetobacter and Gluconobacter were influenced by different temperatures. Furthermore, high temperature helped maintain low octanoic and hexanoic acids. Subsequently, we found that high temperature improved total amino acids and iridoid glycosides. The correlation network analysis revealed that bacterial communities impacted the quality (volatile flavours, amino acid profiles, and iridoid glycosides) of fermented noni fruit. Overall, altering the temperature induced variations in microbial communities and quality during the noni fruit fermentation process. These results are instrumental in the pursuit of quality control in natural fermentation processes.},
}
@article {pmid39182764,
year = {2024},
author = {Zhao, Y and Tan, J and Fang, L and Jiang, L},
title = {Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175732},
doi = {10.1016/j.scitotenv.2024.175732},
pmid = {39182764},
issn = {1879-1026},
mesh = {*Methane/metabolism ; Animals ; *Ruminants ; Metabolomics ; Metagenomics ; Air Pollutants/analysis ; Greenhouse Gases ; Rumen/metabolism ; Gastrointestinal Microbiome ; Genomics ; },
abstract = {Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.},
}
@article {pmid39181265,
year = {2024},
author = {Dong, W and Zhou, J and Zhang, CJ and Yang, Q and Li, M},
title = {Methylotrophic substrates stimulated higher methane production than competitive substrates in mangrove sediments.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175677},
doi = {10.1016/j.scitotenv.2024.175677},
pmid = {39181265},
issn = {1879-1026},
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; China ; Microbiota ; Bacteria/metabolism/classification ; },
abstract = {Although mangrove forests can uptake atmospheric CO2 and store carbon as organic matter called "blue carbon", it is also an important natural source of greenhouse gas methane. Methanogens are major contributors to methane and play important roles in the global carbon cycle. However, our understanding of the key microbes and metabolic pathways responsible for methanogenesis under specific substrates in mangrove sediments is still very limited. Here, we set an anaerobic incubation to evaluate the responses of methanogens in mangrove sediments from South China to the addition of diverse methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanethiol (MT)) and further investigated the dynamics of the whole microbial community. Our results showed that diverse substrates stimulated methanogenic activities at different times. The stimulation of methanogenesis was more pronounced at early and late periods by the addition of methylotrophic substrates TMA and MT, respectively. The amplicon sequencing analysis showed that genus Methanococcoides was mainly responsible for TMA-utilized methanogenesis in mangrove sediment, while the multitrophic Methanococcus was most abundant in H2/CO2 and MT treatments. Apart from that, the bacteria enrichments of Syntrophotalea, Clostridium_sensu_stricto_12, Fusibacter in MT treatments might also be associated with the stimulation of methane production. In addition, the metagenomic analysis suggested that Methanosarcinaceae was also one of the key methanogens in MT treatments with different genomic information compared to that in TMA treatments. Finally, the total relative abundances of methanogenesis-related genes were also highest in TMA and MT treatments. These results will help advance our understanding of the contributions of different methanogenesis pathways and methanogens to methane emissions in mangrove sediments.},
}
@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}
@article {pmid39153624,
year = {2024},
author = {Barquero, MB and García-Díaz, C and Dobbler, PT and Jehmlich, N and Moreno, JL and López-Mondéjar, R and Bastida, F},
title = {Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175571},
doi = {10.1016/j.scitotenv.2024.175571},
pmid = {39153624},
issn = {1879-1026},
mesh = {*Zea mays ; *Phosphorus/metabolism ; *Fertilizers ; *Soil Microbiology ; Microbiota ; Bacteria/metabolism ; Agriculture/methods ; Archaea/physiology/metabolism ; Soil/chemistry ; },
abstract = {Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.},
}
@article {pmid39151617,
year = {2024},
author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Sánchez-Porro, C and Ventosa, A},
title = {Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175497},
doi = {10.1016/j.scitotenv.2024.175497},
pmid = {39151617},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; *Archaea/genetics ; Soil/chemistry ; Spain ; Salinity ; Metagenome ; Metagenomics ; },
abstract = {Saline soils and their microbial communities have recently been studied in response to ongoing desertification of agricultural soils caused by anthropogenic impacts and climate change. Here we describe the prokaryotic microbiota of hypersaline soils in the Odiel Saltmarshes Natural Area of Southwest Spain. This region has been strongly affected by mining and industrial activity and feature high levels of certain heavy metals. We sequenced 18 shotgun metagenomes through Illumina NovaSeq from samples obtained from three different areas in 2020 and 2021. Taxogenomic analyses demonstrate that these soils harbored equal proportions of archaea and bacteria, with Methanobacteriota, Pseudomonadota, Bacteroidota, Gemmatimonadota, and Balneolota as most abundant phyla. Functions related to the transport of heavy metal outside the cytoplasm are among the most relevant features of the community (i.e., ZntA and CopA enzymes). They seem to be indispensable to avoid the increase of zinc and copper concentration inside the cell. Besides, the archaeal phylum Methanobacteriota is the main arsenic detoxifier within the microbiota although arsenic related genes are widely distributed in the community. Regarding the osmoregulation strategies, "salt-out" mechanism was identified in part of the bacterial population, whereas "salt-in" mechanism was present in both domains, Bacteria and Archaea. De novo biosynthesis of two of the most universal compatible solutes was detected, with predominance of glycine betaine biosynthesis (betAB genes) over ectoine (ectABC genes). Furthermore, doeABCD gene cluster related to the use of ectoine as carbon and energy source was solely identified in Pseudomonadota and Methanobacteriota.},
}
@article {pmid39150504,
year = {2024},
author = {Sessa, R and Filardo, S and Viscardi, MF and Brandolino, G and Muzii, L and Di Pietro, M and Porpora, MG},
title = {Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study.},
journal = {Archives of gynecology and obstetrics},
volume = {310},
number = {4},
pages = {2141-2151},
pmid = {39150504},
issn = {1432-0711},
mesh = {Humans ; Female ; *Endometriosis/microbiology ; Adult ; *Vagina/microbiology ; Cross-Sectional Studies ; Italy ; *Microbiota ; Young Adult ; Dysbiosis/microbiology ; Bacteria/isolation & purification/classification/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: This cross-sectional study aims to assess the interplay between the vaginal microbiota and endometriosis.<br><br>METHODS: 123 consecutive Italian fertile women, aged between 20 and 40&#xa0;years old, were enrolled during a routine gynecological consultation; 24 were diagnosed with endometriosis and 99 did not complain of any gynecological disease. All women underwent a vaginal swab for the evaluation of the composition and diversity of vaginal microbiota by means of 16&#xa0;s rDNA metagenomic sequencing.<br><br>RESULTS: Compared to women with no gynecological disease, the vaginal microbiota in women with endometriosis showed a similar abundance of Lactobacillus spp.; however, a statistically significant lower abundance in the genera Pseudomonas (p&#x2009;<&#x2009;0.01), Bifidobacterium (p&#x2009;<&#x2009;0.05), Novispirillum (p&#x2009;<&#x2009;0.0000001) and Sphingomonas (p&#x2009;<&#x2009;0.0000001), and a statistically significant increase in the abundance of the genera Escherichia (p&#x2009;<&#x2009;0.00001), Megasphaera (p&#x2009;<&#x2009;0.00001), and Sneathia (p&#x2009;<&#x2009;0.0001) were observed.<br><br>CONCLUSIONS: There is a complex interplay between vaginal microbiota composition and endometriosis, showing a distinct microbial signature in the bacterial genera usually found in dysbiosis.},
}
@article {pmid39147055,
year = {2024},
author = {Lu, J and Qing, C and Huang, X and Zeng, J and Zheng, Y and Xia, P},
title = {Seasonal dynamics and driving mechanisms of microbial biogenic elements cycling function, assembly process, and co-occurrence network in plateau lake sediments.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175510},
doi = {10.1016/j.scitotenv.2024.175510},
pmid = {39147055},
issn = {1879-1026},
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Seasons ; *Phosphorus/analysis ; *Microbiota ; *Nitrogen/analysis ; China ; Environmental Monitoring ; Bacteria/classification/genetics ; Carbon/analysis/metabolism ; },
abstract = {Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43-44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91-99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes.},
}
@article {pmid39128520,
year = {2024},
author = {Wang, C and Zhu, J and Wang, H and Zhang, L and Li, Y and Zhang, Y and Wu, Z and Zhou, Q},
title = {Sedimentary organic matter load influences the ecological effects of submerged macrophyte restoration through rhizosphere metabolites and microbial communities.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175419},
doi = {10.1016/j.scitotenv.2024.175419},
pmid = {39128520},
issn = {1879-1026},
mesh = {*Rhizosphere ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; Lakes ; Phosphorus/metabolism ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; },
abstract = {Organic matter (OM) accumulation in lake sediments has doubled owing to human activities over the past 100 years, which has negatively affected the restoration of submerged vegetation and ecological security. Changes in the pollution structure of sediments caused by plant recovery and rhizosphere chemical processes under different sediment OM levels are the theoretical basis for the rational application of plant rehabilitation technology in lake management. This study explored how Vallisneria natans mediates changes in sediment N and P through rhizospheric metabolites and microbial community and function under low (4.94 %) and high (17.35 %) sediment OM levels. V. natans promoted the accumulation of NH4-N in the high-OM sediment and the transformation of Fe/Al-P to Ca-P in the low-OM sediment. By analyzing 63 rhizospheric metabolites and the sediment microbial metagenome, the metabolites lactic acid and 3-hydroxybutyric acid and the genus Anammoximicrobium were found to mediate NH4-N accumulation in the high-OM sediment. Additionally, 3-hydroxy-decanoic acid, adipic acid, and the genus Bdellovibrionaceae mediated the transformation of Fe/Al-P to Ca-P in the low-OM sediment. The growth of V. natans enriched the abundance of functional genes mediating each step from nitrate to ammonia and the genes encoding urease in the high-OM sediment, and it up-regulated three genes related to microbial phosphorus uptake in the low-OM sediment. This study revealed the necessity of controlling endogenous pollution by recovering submerged macrophytes under high- and low-OM conditions from the perspective of the transformation of inorganic nitrogen and phosphorus.},
}
@article {pmid38914350,
year = {2024},
author = {Akram, J and Song, C and El Mashad, HM and Chen, C and Zhang, R and Liu, G},
title = {Advances in microbial community, mechanisms and stimulation effects of direct interspecies electron transfer in anaerobic digestion.},
journal = {Biotechnology advances},
volume = {76},
number = {},
pages = {108398},
doi = {10.1016/j.biotechadv.2024.108398},
pmid = {38914350},
issn = {1873-1899},
mesh = {Electron Transport ; Anaerobiosis ; *Microbiota/physiology ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Methane/metabolism ; },
abstract = {Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes.},
}
@article {pmid39256724,
year = {2024},
author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN},
title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {1124},
pmid = {39256724},
issn = {1471-2407},
support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; *Feces/microbiology ; Female ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Asian People ; Colon/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; },
abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.<br><br>METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n&#x2009;=&#x2009;112) and colonic tissue (n&#x2009;=&#x2009;36) in 112 individuals. The cohort comprised of individuals with CRC (n&#x2009;=&#x2009;24), premalignant lesions (n&#x2009;=&#x2009;10), healthy individuals (n&#x2009;=&#x2009;50) and in those with diabetes (n&#x2009;=&#x2009;28).<br><br>RESULTS: Overall, the relative abundances of genus Fusobacterium (p&#x2009;<&#x2009;0.001), Acinetobacter (p&#x2009;<&#x2009;0.001), Escherichia-Shigella (p&#x2009;<&#x2009;0.05) were significantly higher in gut tissue, while Romboutsia (p&#x2009;<&#x2009;0.01) and Prevotella (p&#x2009;<&#x2009;0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p&#x2009;<&#x2009;0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p&#x2009;<&#x2009;0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.<br><br>CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.},
}
@article {pmid39256682,
year = {2024},
author = {Wu, LH and Hu, CX and Liu, TX},
title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {337},
pmid = {39256682},
issn = {1471-2180},
mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.<br><br>METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.<br><br>RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-&#x3b2;-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.<br><br>CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.},
}
@article {pmid39256599,
year = {2024},
author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP},
title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21168},
pmid = {39256599},
issn = {2045-2322},
support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; },
abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.},
}
@article {pmid39232160,
year = {2024},
author = {Chen, J and Jia, Y and Sun, Y and Liu, K and Zhou, C and Liu, C and Li, D and Liu, G and Zhang, C and Yang, T and Huang, L and Zhuang, Y and Wang, D and Xu, D and Zhong, Q and Guo, Y and Li, A and Seim, I and Jiang, L and Wang, L and Lee, SMY and Liu, Y and Wang, D and Zhang, G and Liu, S and Wei, X and Yue, Z and Zheng, S and Shen, X and Wang, S and Qi, C and Chen, J and Ye, C and Zhao, F and Wang, J and Fan, J and Li, B and Sun, J and Jia, X and Xia, Z and Zhang, H and Liu, J and Zheng, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Xu, X and Mock, T and Li, S and Zhang, W and Fan, G},
title = {Global marine microbial diversity and its potential in bioprospecting.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {371-379},
pmid = {39232160},
issn = {1476-4687},
mesh = {*CRISPR-Cas Systems/genetics ; *Bioprospecting ; *Biodiversity ; *Aquatic Organisms/genetics ; Bacteria/genetics/classification ; Archaea/genetics/classification ; Genome, Bacterial/genetics ; Metagenome ; Genome, Archaeal/genetics ; Seawater/microbiology ; Phylogeny ; Oceans and Seas ; },
abstract = {The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems[1,2]. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications[3,4]. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.},
}
@article {pmid39186442,
year = {2024},
author = {Chen, Y and Ma, W and Zhao, J and Stanton, C and Ross, RP and Zhang, H and Chen, W and Yang, B},
title = {Lactobacillus plantarum Ameliorates Colorectal Cancer by Ameliorating the Intestinal Barrier through the CLA-PPAR-γ Axis.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {36},
pages = {19766-19785},
doi = {10.1021/acs.jafc.4c02824},
pmid = {39186442},
issn = {1520-5118},
mesh = {*Lactobacillus plantarum/metabolism ; *PPAR gamma/metabolism/genetics ; Animals ; Mice ; *Colorectal Neoplasms/metabolism ; Humans ; *Probiotics/administration &amp; dosage/pharmacology ; Male ; *Linoleic Acids, Conjugated/pharmacology/metabolism ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/metabolism/microbiology ; Female ; NF-kappa B/metabolism/genetics ; Apoptosis/drug effects ; Claudin-1/metabolism/genetics ; Zonula Occludens-1 Protein/metabolism/genetics ; },
abstract = {Colorectal cancer (CRC) is the third-largest cancer worldwide. Lactobacillus can regulate the intestinal barrier and gut microbiota. However, the mechanisms of Lactobacillus that alleviate CRC remained unknown. This study aimed to explore the regulatory effect of Lactobacillus plantarum on CRC and its potential mechanism. CCFM8661 treatment significantly ameliorated CRC compared with phosphate-buffered solution (PBS) treatment in Apc[Min/+] mice. In addition, conjugated linoleic acid (CLA) was proved to be the key metabolite for CCFM8661 in ameliorating CRC by molecular biology techniques. Peroxisome proliferator-activated receptor γ (PPAR-γ) was proved to be the key receptor in ameliorating CRC by inhibitor intervention experiments. Moreover, supplementation with CCFM8661 ameliorated CRC by producing CLA to inhibit NF-κB pathway and pro-inflammatory cytokines, up-regulate ZO-1, Claudin-1, and MUC2, and promote tumor cell apoptosis in a PPAR-γ-dependent manner. Metagenomic analysis showed that CCFM8661 treatment significantly increased Odoribacter splanchnicus, which could ameliorate CRC by repairing the intestinal barrier. Clinical results showed that intestinal CLA, butyric acid, PPAR-γ, and Lactobacillus were significantly decreased in CRC patients, and these indicators were significantly negatively correlated with CRC. CCFM8661 alleviated CRC by ameliorating the intestinal barrier through the CLA-PPAR-γ axis. These results will promote the development of dietary probiotic supplements for CRC.},
}
@article {pmid39154602,
year = {2024},
author = {García-Roldán, A and de la Haba, RR and Sánchez-Porro, C and Ventosa, A},
title = {'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127869},
doi = {10.1016/j.micres.2024.127869},
pmid = {39154602},
issn = {1618-0623},
mesh = {*Metagenomics ; *Bacteria/genetics/classification ; *Salinity ; *Archaea/genetics/classification ; Spain ; Seawater/microbiology ; Phylogeny ; Atlantic Ocean ; Biodiversity ; Salts ; Microbiota/genetics ; Ecosystem ; Metagenome ; },
abstract = {Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.},
}
@article {pmid39122162,
year = {2024},
author = {Liu, S and Hou, C and Dong, C and Zhao, D and Chen, Q and Terence Yang, JY and Tang, K},
title = {Integrated multi-omics analyses reveal microbial community resilience to fluctuating low oxygen in the East China sea.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119764},
doi = {10.1016/j.envres.2024.119764},
pmid = {39122162},
issn = {1096-0953},
mesh = {*Oxygen/metabolism/analysis ; China ; *Seawater/microbiology/chemistry ; *Microbiota ; Proteomics ; Bacteria/metabolism/genetics ; Metagenomics ; Oceans and Seas ; Multiomics ; },
abstract = {Climate change and eutrophication are accelerating ocean deoxygenation, leading to a global decline in oxygen levels. The East China Sea, frequently experiencing deoxygenation events, harbors diverse microbial communities. However, the response of these communities to the changing deoxygenation dynamics remains poorly understood. Here, we explored the composition and function of microbial communities inhabiting seawaters of the Changjiang Estuary and offshore areas. Our findings suggested that neutral processes significantly influenced the assembly of these communities. The overall bacterial composition demonstrated remarkable high stability across the oxygen gradient. Salinity exhibited a significantly stronger correlation with bacterial community structure than dissolved oxygen. Both metagenomics and metaproteomics revealed that all of the samples exhibited similar functional community structures. Heterotrophic metabolism dominated these sites, as evidenced by a diverse array of transporters and metabolic enzymes for organic matter uptake and utilization, which constituted a significant portion of the expressed proteins. O2 was the primary electron acceptor in bacteria even under hypoxic conditions, evidenced by expression of low- and high-affinity cytochrome oxidases. Proteins associated with anaerobic processes, such as dissimilatory sulfite reductases, were virtually undetectable. Untargeted liquid chromatography with tandem mass spectrometry analysis of seawater samples revealed a diverse range of dissolved organic matter (DOM) components in amino acids, lipids, organic acids, peptides, and carbohydrates, potentially fueling dominant taxa growth. Despite fluctuations in the abundance of specific genera, the remarkable similarity in community structure, function, and DOM suggests that this ecosystem possesses robust adaptive mechanisms that buffer against abrupt changes, even below the well-defined hypoxic threshold in marine ecosystem.},
}
@article {pmid39094895,
year = {2024},
author = {Shi, Z and Zhang, C and Sun, M and Usman, M and Cui, Y and Zhang, S and Ni, B and Luo, G},
title = {Syntrophic propionate degradation in anaerobic digestion facilitated by hydrochar: Microbial insights as revealed by genome-centric metatranscriptomics.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119717},
doi = {10.1016/j.envres.2024.119717},
pmid = {39094895},
issn = {1096-0953},
mesh = {*Propionates/metabolism ; Anaerobiosis ; *Methane/metabolism ; Transcriptome ; Bacteria/metabolism/genetics ; Microbiota ; },
abstract = {Propionate is a model substrate for studying energy-limited syntrophic communities in anaerobic digestion, and syntrophic bacteria usually catalyze its degradation in syntrophy with methanogens. In the present study, metagenomics and metatranscriptomics were used to study the effect of the supportive material (e.g., hydrochar) on the key members of propionate degradation and their cooperation mechanism. The results showed that hydrochar increased the methane production rate (up to 57.1%) from propionate. The general transcriptional behavior of the microbiome showed that both interspecies H2 transfer (IHT) and direct interspecies electron transfer (DIET) played essential roles in the hydrochar-mediated methanation of propionate. Five highly active syntrophic propionate-oxidizing bacteria were identified by genome-centric metatranscriptomics. H85pel, a member of the family Pelotomaculaceae, was specifically enriched by hydrochar. Hydrochar enhanced the expression of the flagellum subunit, which interacted with methanogens and hydrogenases in H85pel, indicating that IHT was one of the essential factors promoting propionate degradation. Hydrochar also enriched H162tha belonging to the genus of Thauera. Hydrochar induced the expression of genes related to the complete propionate oxidation pathway, which did not produce acetate. Hydrochar and e-pili-mediated DIET were enhanced, which was another factor promoting propionate degradation. These findings improved the understanding of metabolic traits and cooperation between syntrophic propionate oxidizing bacteria (SPOB) and co-metabolizing partners and provided comprehensive transcriptional insights on function in propionate methanogenic systems.},
}
@article {pmid39074770,
year = {2024},
author = {Gao, T and Wang, Y and Lai, J and Wang, F and Yao, G and Bao, S and Liu, J and Wan, X and Chen, C and Zhang, Y and Jiang, H and Jiang, S and Han, P},
title = {Effects of nitrile compounds on the structure and function of soil microbial communities as revealed by metagenomes.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119700},
doi = {10.1016/j.envres.2024.119700},
pmid = {39074770},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Nitriles/toxicity ; *Soil Pollutants/toxicity ; *Metagenome/drug effects ; Microbiota/drug effects ; Bacteria/drug effects/genetics ; },
abstract = {The proliferation of nitrile mixtures has significantly exacerbated environmental pollution. This study employed metagenomic analysis to investigate the short-term effects of nitrile mixtures on soil microbial communities and their metabolic functions. It also examined the responses of indigenous microorganisms and their functional metabolic genes across various land use types to different nitrile stressors. The nitrile compound treatments in this study resulted in an increase in the abundance of Proteobacteria, Actinobacteria, and Firmicutes, while simultaneously reducing overall microbial diversity. The key genes involved in the denitrification process, namely, nirK, nosZ, and hao, were down-regulated, and NO3[-]-N, NO2[-]-N, and NH4[+]-N concentrations decreased by 7.7%-12.3%, 11.1%-21.3%, and 11.3%-30.9%, respectively. Notably, pond sludge samples exhibited a significant increase in the abundance of nitrogen fixation-related genes nifH, vnfK, vnfH, and vnfG following exposure to nitrile compounds. Furthermore, the fumarase gene fumD, which is responsible for catalyzing fumaric acid into malic acid in the tricarboxylic acid cycle, showed a substantial increase of 7.2-10.6-fold upon nitrile addition. Enzyme genes associated with the catechol pathway, including benB-xylY, dmpB, dmpC, dmpH, and mhpD, displayed increased abundance, whereas genes related to the benzoyl-coenzyme A pathway, such as bcrA, dch, had, oah, and gcdA, were notably reduced. In summary, complex nitrile compounds were found to significantly reduce the species diversity of soil microorganisms. Nitrile-tolerant microorganisms demonstrated the ability to degrade and adapt to nitrile pollutants by enhancing functional enzymes involved in the catechol pathway and fenugreek conversion pathway. This study offers insights into the specific responses of microorganisms to compound nitrile contamination, as well as valuable information for screening nitrile-degrading microorganisms and identifying nitrile metabolic enzymes.},
}
@article {pmid39043353,
year = {2024},
author = {Thacharodi, A and Hassan, S and Ahmed, ZHT and Singh, P and Maqbool, M and Meenatchi, R and Pugazhendhi, A and Sharma, A},
title = {The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119661},
doi = {10.1016/j.envres.2024.119661},
pmid = {39043353},
issn = {1096-0953},
mesh = {*Methane/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Ruminants/microbiology ; Rumen/microbiology/metabolism ; Greenhouse Gases/metabolism ; Probiotics ; Cattle ; Fermentation ; Bacteria/metabolism ; },
abstract = {Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.},
}
@article {pmid38519004,
year = {2024},
author = {Sepulveda, M and Rasic, M and Lei, YM and Kwan, M and Chen, L and Chen, Y and Perkins, D and Alegre, ML},
title = {Coordinated elimination of bacterial taxa optimally attenuates alloimmunity and prolongs allograft survival.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {24},
number = {9},
pages = {1573-1582},
doi = {10.1016/j.ajt.2024.03.020},
pmid = {38519004},
issn = {1600-6143},
support = {T32 AI007090/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Graft Survival/immunology/drug effects ; *Graft Rejection/immunology/prevention &amp; control ; *Gastrointestinal Microbiome/immunology ; *Skin Transplantation ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; Allografts ; Male ; },
abstract = {This study aimed to dissect the relationship between specific gut commensal bacterial subgroups, their functional metabolic pathways, and their impact on skin allograft outcome and alloimmunity. We previously showed that oral broad-spectrum antibiotic (Abx) pretreatment in mice delayed skin, heart, and lung allograft rejection and dampened alloimmune responses. Here, rationally designed Abx combinations targeting major bacterial groups were used to elucidate their individual contribution to modulating alloimmune responses. Abx cocktails targeting intestinal gram-negative, gram-positive, or anaerobic/gram-positive bacteria by oral gavage, all delayed skin allograft rejection, and reduced alloreactive T cell priming to different extents. Notably, the most pronounced extension of skin allograft survival and attenuation of alloimmunity were achieved when all gut bacterial groups were simultaneously targeted. These results suggest a model in which the strength of the alloimmune response is additively tuned up by gut microbial diversity. Shotgun metagenomic sequencing enabled strain-level resolution and identified a shared commensal, Parabacteroides distasonis, as the most enriched following all Abx treatments. Oral administration of P.distasonis to mice harboring a diverse microbiota significantly prolonged skin allograft survival, identifying a probiotic with therapeutic benefit in transplantation.},
}
@article {pmid39256479,
year = {2024},
author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M},
title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {989},
pmid = {39256479},
issn = {2052-4463},
mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; },
abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.},
}
@article {pmid39256206,
year = {2024},
author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO},
title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {918},
pmid = {39256206},
issn = {1573-2959},
mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; },
abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.},
}
@article {pmid39255397,
year = {2024},
author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R},
title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S95-S108},
doi = {10.1093/infdis/jiae165},
pmid = {39255397},
issn = {1537-6613},
support = {//Infectious Diseases Society of America/ ; //Foundation/ ; 23A02//Florida Department of Health/ ; 440658//US Department of Agriculture/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; R01 AG070094/NH/NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.<br><br>METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.<br><br>RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.<br><br>CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.},
}
@article {pmid39254265,
year = {2024},
author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N},
title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2398126},
doi = {10.1080/19490976.2024.2398126},
pmid = {39254265},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation &amp; purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; },
abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.},
}
@article {pmid39252078,
year = {2024},
author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S},
title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {67},
pmid = {39252078},
issn = {2524-6372},
support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; },
abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.<br><br>RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel &#x3b2;-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.<br><br>CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.},
}
@article {pmid39154578,
year = {2024},
author = {Liang, T and Liu, Y and Guo, N and Li, Y and Niu, L and Liu, J and Ma, Q and Zhang, J and Shan, M},
title = {Jinhong decoction ameliorates injury in septic mice without disrupting the equilibrium of gut microbiota.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {251},
number = {},
pages = {116404},
doi = {10.1016/j.jpba.2024.116404},
pmid = {39154578},
issn = {1873-264X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Sepsis/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Male ; *Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; Chromatography, High Pressure Liquid/methods ; Cecum/microbiology ; Mice, Inbred C57BL ; },
abstract = {Sepsis is a life-threatening condition and usually be treated with antibiotics, which however often has severe side effects. This work proposed a novel Chinese traditional medicine JINHONG (JH) decoction for therapy of sepsis. We first identified the chemical constituents of JH decoction by using high-performance liquid chromatography and mass spectrometry (HPLC-MS). Then, we constructed a model mouse for sepsis by using cecal ligation and puncture (CLP). Metagenomic sequencing method was used to compare the diversity and abundance of the gut microbiota between normal, disease model, JH decoction-treatment and antibiotic-treatment mice. Many indices including the number of platelets, CD62p and CD63 content, AQP2 and AQP8 level, as well as the expression level of protein C confirmed that the sepsis resulted in serious pathological damage, while all of these indices could be reversed by JH decoction and antibiotics. The diversity and abundance of intestinal flora decreased in CLP mice, and the decrements aggravated after antibiotic treatment while can be recovered by JH decoction treatment. The abundance of anti-inflammatory Ruminococcaceae increased after JH decoction treatment, indicating that JH decoction could ameliorate pathology associated with sepsis in CLP model via modulating the intestinal flora. This study demonstrates that JH decoction could treat sepsis clinically without obvious adverse effects on gut microbiota.},
}
@article {pmid39101654,
year = {2024},
author = {Wang, XX and Liu, YT and Ren, JG and Liu, HM and Fu, Q and Yang, Y and Fu, QY and Chen, G},
title = {Salivary Microbiome Relates to Neoadjuvant Immunotherapy Response in OSCC.},
journal = {Journal of dental research},
volume = {103},
number = {10},
pages = {988-998},
doi = {10.1177/00220345241262759},
pmid = {39101654},
issn = {1544-0591},
mesh = {Humans ; *Saliva/microbiology/immunology ; *Mouth Neoplasms/therapy/microbiology/immunology ; Male ; Female ; *Neoadjuvant Therapy ; *Microbiota ; Middle Aged ; *Immunotherapy/methods ; *Carcinoma, Squamous Cell/therapy/immunology/microbiology ; Aged ; Treatment Outcome ; Adult ; },
abstract = {Most patients diagnosed with oral squamous cell carcinoma (OSCC) present with locally advanced stages, which are typically associated with poor outcomes. Although immunotherapy offers potential improvements in patient survival, its efficacy is hampered by low response rates. The microbiome is widely involved in tumor immunity and may play a role in immunotherapy. This study aimed to investigate the potential association between the oral (salivary) microbiome and immunotherapy response in patients with OSCC. Salivary metagenome sequencing was performed on 47 patients with OSCC undergoing neoadjuvant immunotherapy (NAIT) in a clinical trial (NCT04649476). Patients were divided into responders and nonresponders based on their pathological responses. The results showed that the species richness of the salivary microbiome was lower in the nonresponders before NAIT than in the responders. Differential analysis revealed that nonresponders exhibited a lower relative abundance of 34 bacterial species and a higher relative abundance of 4 bacterial species. Notably, low levels of Eubacterium infirmum, Actinobaculum, and Selenomas (EAS) in the saliva may be associated with the nonresponse of patients with OSCC to NAIT. A nomogram based on EAS was developed and validated to determine the efficacy of NAIT. The area under the curve for the training cohort was 0.81 (95% confidence interval, 0.66 to 0.81). Quantitative polymerase chain reaction confirmed that low levels of salivary EAS effectively identified nonresponders to NAIT. Furthermore, the low abundance of salivary EAS was closely correlated with a low density of intratumoral CD4[+], CD14[+], CD68[+], and FOXP3[+] cells. Metabolic functional annotation revealed numerous biosynthetic processes associated with EAS that were more active in responders. In summary, this study provides valuable data resources for the salivary microbiome and reveals that nonresponders have different salivary microbiome profiles than responders do before NAIT. Low salivary EAS levels can serve as potential biomarkers for distinguishing nonresponders from responders.},
}
@article {pmid39251745,
year = {2024},
author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M},
title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21034},
pmid = {39251745},
issn = {2045-2322},
support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; },
mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; },
abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.},
}
@article {pmid39251728,
year = {2024},
author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M},
title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21025},
pmid = {39251728},
issn = {2045-2322},
support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; },
mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adolescent ; Multiomics ; },
abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.},
}
@article {pmid39250478,
year = {2024},
author = {Pusa, T and Rousu, J},
title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0309921},
doi = {10.1371/journal.pone.0309921},
pmid = {39250478},
issn = {1932-6203},
mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.},
}
@article {pmid39250184,
year = {2024},
author = {Pallen, MJ},
title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006508},
pmid = {39250184},
issn = {1466-5034},
mesh = {*Bacteria/genetics/classification ; *Phylogeny ; Archaea/genetics/classification ; History, 20th Century ; History, 21st Century ; Prokaryotic Cells/classification ; Classification/methods ; },
abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.},
}
@article {pmid39247916,
year = {2024},
author = {Lyu, X and Xu, X and Shen, S and Qin, F},
title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1452999},
pmid = {39247916},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; *Mendelian Randomization Analysis ; *Genome-Wide Association Study ; *Saliva/microbiology ; *Asian People/genetics ; *Microbiota/genetics ; Mouth/microbiology ; Asia, Eastern/epidemiology ; Tongue/microbiology ; Genetic Predisposition to Disease ; East Asian People ; },
abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.<br><br>METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).<br><br>RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.<br><br>DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.},
}
@article {pmid39245657,
year = {2024},
author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {80},
pmid = {39245657},
issn = {2055-5008},
support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; },
abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.},
}
@article {pmid39216430,
year = {2024},
author = {Gupta, A and Shivachandran, A and Saleena, LM},
title = {Oral microbiome insights: Tracing acidic culprits in dental caries with functional metagenomics.},
journal = {Archives of oral biology},
volume = {168},
number = {},
pages = {106064},
doi = {10.1016/j.archoralbio.2024.106064},
pmid = {39216430},
issn = {1879-1506},
mesh = {*Dental Caries/microbiology ; Humans ; *Metagenomics/methods ; *Microbiota ; Mouth/microbiology ; Acids/metabolism ; Bacteria/classification/genetics ; DNA, Bacterial ; Sequence Analysis, DNA ; Male ; Female ; },
abstract = {OBJECTIVE: This study aimed to investigate the presence and abundance of acid-producing bacteria in dental caries samples using functional gene prediction techniques.<br><br>DESIGN: A total of 24 dental caries samples were collected for analysis. DNA isolation was performed followed by shotgun metagenomic sequencing. Functional gene prediction techniques were used to identify enzymes responsible for acid production from primary metabolites. Enzymes responsible for converting primary metabolites into acids were identified from the KEGG database. Subsequently, 840 contigs were examined, and their genus and species were characterized.<br><br>RESULTS: Analysis of the obtained data revealed 31 KEGG IDs corresponding to enzymes involved in the conversion of primary metabolites into acids. All 117 identified genera from the contig analysis were found to be part of the oral microbiome. In addition, A higher prevalence of acid-producing bacteria was noted in dental caries samples compared to earlier reports.<br><br>CONCLUSION: The study indicates the significant role of acid-producing bacteria in the initiation and progression of dental caries. The findings highlight the importance of microbial activity in the demineralization process of tooth enamel. Methods for preventing dental decay may be promising if specific measures are implemented to reduce the amount of acid produced by oral bacteria.},
}
@article {pmid39084550,
year = {2024},
author = {Kwon, M and Nilufar Zakhidovna, R and Boymaxmat Abdiazizovich, K and Jung, C and Kil, EJ},
title = {First metagenomic analysis of virome in Uzbekistan honey bee (Apis mellifera): Investigating basic information on honey bee viruses.},
journal = {Journal of invertebrate pathology},
volume = {206},
number = {},
pages = {108171},
doi = {10.1016/j.jip.2024.108171},
pmid = {39084550},
issn = {1096-0805},
mesh = {Bees/virology ; Animals ; *Virome ; Uzbekistan ; *Insect Viruses/genetics/classification/isolation &amp; purification ; Metagenomics ; },
abstract = {Honey bees are economically important insects. However, they face multiple biotic and abiotic stresses, such as diseases, pesticides, climate change, and pests, which cause the loss of honey bee colonies worldwide. Among these factors, viruses have been identified as the major cause of colony loss. Research on honey bee viruses in Uzbekistan is limited. This study investigated the viruses affecting honey bees in Uzbekistan. Virome analysis was conducted for each sample using high-throughput sequencing and bioinformatics. Nine honey bee viruses have been identified: the acute bee paralysis virus, aphid lethal paralysis virus, Apis rhabdovirus 1 and 2, black queen cell virus, deformed wing virus, Lake Sinai virus 10, sacbrood virus, and Hubei partiti-like virus 34. Additionally, 15 plant viruses were identified, 7 of which were novel. This study is the first virome analysis of Uzbekistan honey bees and provides a foundation for understanding the viruses affecting honey bees and plants in Uzbekistan.},
}
@article {pmid39033688,
year = {2024},
author = {Berryman, MA and Ilonen, J and Triplett, EW and Ludvigsson, J},
title = {Functional metagenomic analysis reveals potential inflammatory triggers associated with genetic risk for autoimmune disease.},
journal = {Journal of autoimmunity},
volume = {148},
number = {},
pages = {103290},
doi = {10.1016/j.jaut.2024.103290},
pmid = {39033688},
issn = {1095-9157},
mesh = {Humans ; *Autoimmune Diseases/immunology/etiology/genetics/microbiology ; *Metagenomics/methods ; *Genetic Predisposition to Disease ; Infant ; Female ; Sweden/epidemiology ; Male ; Feces/microbiology ; Haplotypes ; Inflammation/immunology/genetics ; Gastrointestinal Microbiome/immunology ; HLA-DQ Antigens/genetics/immunology ; Flagellin/immunology ; Prevotella/immunology/genetics ; Genotype ; },
abstract = {To assess functional differences between the microbiomes of individuals with autoimmune risk-associated human leukocyte antigen (HLA) genetics and autoimmune protection-associated HLA, we performed a metagenomic analysis of stool samples from 72 infants in the All Babies in Southeast Sweden general-population cohort and assessed haplotype-peptide binding affinities. Infants with risk-associated HLA DR3-DQ2.5 and DR4-DQ8 had a higher abundance of known pathogen-associated molecular patterns and virulence related genes than infants with protection-associated HLA DR15-DQ6.2. However, there was limited overlap in the type of inflammatory trigger between risk groups. Supported by a high Firmicutes/Bacteroides ratio and differentially abundant flagellated species, genes related to the synthesis of flagella were prominent in those with HLA DR3-DQ2.5. However, this haplotype had a significantly lower likelihood of binding affinity to flagellin peptides. O-antigen biosynthesis genes were significantly correlated with the risk genotypes and absent from protective genotype association, supported by the differential abundance of gram-negative bacteria seen in the risk-associated groups. Genes related to vitamin B biosynthesis stood out in higher abundance in infants with HLA DR3-DQ2.5/DR4-DQ8 heterozygosity compared to those with autoimmune-protective genetics. Prevotella species and genus were significantly abundant in all infant groups with high risk for autoimmune disease. The potential inflammatory triggers associated with genetic risk for autoimmunity have significant implications. These results suggest that certain HLA haplotypes may be creating the opportunity for dysbiosis and subsequent inflammation early in life by clearing beneficial microbes or not clearing proinflammatory microbes. This HLA gatekeeping may prevent genetically at-risk individuals from benefiting from probiotic therapies by restricting the colonization of those beneficial bacteria.},
}
@article {pmid38960582,
year = {2024},
author = {Sun, H and Sun, K and Tian, H and Chen, X and Su, S and Tu, Y and Chen, S and Wang, J and Peng, M and Zeng, M and Li, X and Luo, Y and Xie, Y and Feng, X and Li, Z and Zhang, X and Li, X and Liu, Y and Ye, W and Chen, Z and Zhu, Z and Li, Y and Xia, F and Zhou, H and Duan, C},
title = {Integrated metagenomic and metabolomic analysis reveals distinctive stage-specific gut-microbiome-derived metabolites in intracranial aneurysms.},
journal = {Gut},
volume = {73},
number = {10},
pages = {1662-1674},
doi = {10.1136/gutjnl-2024-332245},
pmid = {38960582},
issn = {1468-3288},
mesh = {*Intracranial Aneurysm/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Male ; Mice ; Female ; *Tryptophan/metabolism/blood ; *Metabolomics/methods ; *Metagenomics/methods ; Middle Aged ; Aneurysm, Ruptured/microbiology/metabolism ; Indican/metabolism/blood ; Biomarkers/blood/metabolism ; Feces/microbiology ; Disease Models, Animal ; Aged ; Disease Progression ; },
abstract = {OBJECTIVE: Our study aimed to explore the influence of gut microbiota and their metabolites on intracranial aneurysms (IA) progression and pinpoint-related metabolic biomarkers derived from the gut microbiome.<br><br>DESIGN: We recruited 358 patients with unruptured IA (UIA) and 161 with ruptured IA (RIA) from two distinct geographical regions for conducting an integrated analysis of plasma metabolomics and faecal metagenomics. Machine learning algorithms were employed to develop a classifier model, subsequently validated in an independent cohort. Mouse models of IA were established to verify the potential role of the specific metabolite identified.<br><br>RESULTS: Distinct shifts in taxonomic and functional profiles of gut microbiota and their related metabolites were observed in different IA stages. Notably, tryptophan metabolites, particularly indoxyl sulfate (IS), were significantly higher in plasma of RIA. Meanwhile, upregulated tryptophanase expression and indole-producing microbiota were observed in gut microbiome of RIA. A model harnessing gut-microbiome-derived tryptophan metabolites demonstrated remarkable efficacy in distinguishing RIA from UIA patients in the validation cohort (AUC=0.97). Gut microbiota depletion by antibiotics decreased plasma IS concentration, reduced IA formation and rupture in mice, and downregulated matrix metalloproteinase-9 expression in aneurysmal walls with elastin degradation reduction. Supplement of IS reversed the effect of gut microbiota depletion.<br><br>CONCLUSION: Our investigation highlights the potential of gut-microbiome-derived tryptophan metabolites as biomarkers for distinguishing RIA from UIA patients. The findings suggest a novel pathogenic role for gut-microbiome-derived IS in elastin degradation in the IA wall leading to the rupture of IA.},
}
@article {pmid38955400,
year = {2024},
author = {Swarte, JC and Zhang, S and Nieuwenhuis, LM and Gacesa, R and Knobbe, TJ and , and De Meijer, VE and Damman, K and Verschuuren, EAM and Gan, TC and Fu, J and Zhernakova, A and Harmsen, HJM and Blokzijl, H and Bakker, SJL and Björk, JR and Weersma, RK and , },
title = {Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients.},
journal = {Gut},
volume = {73},
number = {10},
pages = {1650-1661},
doi = {10.1136/gutjnl-2023-331441},
pmid = {38955400},
issn = {1468-3288},
mesh = {Humans ; *Dysbiosis/mortality ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Organ Transplantation/adverse effects ; Prospective Studies ; Cause of Death ; Transplant Recipients/statistics &amp; numerical data ; Adult ; Feces/microbiology ; Netherlands/epidemiology ; Metagenome ; Aged ; },
abstract = {OBJECTIVE: Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, the relationship with overall survival in specific diseases has not been extensively studied. In the current study, we present results from an in-depth analysis of the relationship between gut dysbiosis and all-cause and cause-specific mortality in the setting of solid organ transplant recipients (SOTR).<br><br>DESIGN: We analysed 1337 metagenomes derived from faecal samples of 766 kidney, 334 liver, 170 lung and 67 heart transplant recipients part of the TransplantLines Biobank and Cohort-a prospective cohort study including extensive phenotype data with 6.5 years of follow-up. To analyze gut dysbiosis, we included an additional 8208 metagenomes from the general population of the same geographical area (northern Netherlands). Multivariable Cox regression and a machine learning algorithm were used to analyse the association between multiple indicators of gut dysbiosis, including individual species abundances, and all-cause and cause-specific mortality.<br><br>RESULTS: We identified two patterns representing overall microbiome community variation that were associated with both all-cause and cause-specific mortality. The gut microbiome distance between each transplantation recipient to the average of the general population was associated with all-cause mortality and death from infection, malignancy and cardiovascular disease. A multivariable Cox regression on individual species abundances identified 23 bacterial species that were associated with all-cause mortality, and by applying a machine learning algorithm, we identified a balance (a type of log-ratio) consisting of 19 out of the 23 species that were associated with all-cause mortality.<br><br>CONCLUSION: Gut dysbiosis is consistently associated with mortality in SOTR. Our results support the observations that gut dysbiosis is associated with long-term survival. Since our data do not allow us to infer causality, more preclinical research is needed to understand mechanisms before we can determine whether gut microbiome-directed therapies may be designed to improve long-term outcomes.},
}
@article {pmid39244633,
year = {2024},
author = {Li, F and Liu, J and Maldonado-Gómez, MX and Frese, SA and Gänzle, MG and Walter, J},
title = {Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {168},
pmid = {39244633},
issn = {2049-2618},
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus reuteri/genetics/classification ; Reproducibility of Results ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Limit of Detection ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.<br><br>RESULTS: Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10[4] cells/g feces) and linearity (R[2]&#x2009;>&#x2009;0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016[&#xa0;T], resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 10[3] cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016[&#xa0;T] during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a&#xa0;much lower LOD&#xa0;and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing).<br><br>CONCLUSIONS: Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.},
}
@article {pmid39244624,
year = {2024},
author = {Yang, X and Feng, K and Wang, S and Yuan, MM and Peng, X and He, Q and Wang, D and Shen, W and Zhao, B and Du, X and Wang, Y and Wang, L and Cao, D and Liu, W and Wang, J and Deng, Y},
title = {Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {166},
pmid = {39244624},
issn = {2049-2618},
support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; },
mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Bioreactors/microbiology ; *Metabolomics ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Methane/metabolism ; Thermodynamics ; Multiomics ; },
abstract = {BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.<br><br>RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.<br><br>CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.},
}
@article {pmid39244357,
year = {2024},
author = {Abo-Ismail, M and Sadek, MAA and Humagain, K and Banjara, N and Pokharel, S},
title = {Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California.},
journal = {Food microbiology},
volume = {124},
number = {},
pages = {104598},
doi = {10.1016/j.fm.2024.104598},
pmid = {39244357},
issn = {1095-9998},
mesh = {Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seasons ; *Soil Microbiology ; *Farms ; California ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Water Microbiology ; Spatio-Temporal Analysis ; Metagenomics ; },
abstract = {This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.},
}
@article {pmid39242698,
year = {2024},
author = {Lu, X and Gong, G and Zhang, Q and Yang, S and Wu, H and Zhao, M and Wang, X and Shen, Q and Ji, L and Liu, Y and Wang, Y and Liu, J and Suolang, S and Ma, X and Shan, T and Zhang, W},
title = {Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1097},
pmid = {39242698},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Tibet ; Metagenome ; },
abstract = {The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.},
}
@article {pmid39179139,
year = {2024},
author = {Gao, N and Zhuang, Y and Zheng, Y and Li, Y and Wang, Y and Zhu, S and Fan, M and Tian, W and Jiang, Y and Wang, Y and Cui, M and Suo, C and Zhang, T and Jin, L and Chen, X and Xu, K},
title = {Investigating the link between gut microbiome and bone mineral density: The role of genetic factors.},
journal = {Bone},
volume = {188},
number = {},
pages = {117239},
doi = {10.1016/j.bone.2024.117239},
pmid = {39179139},
issn = {1873-2763},
mesh = {Humans ; *Bone Density/genetics ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; *Osteoporosis/genetics/microbiology ; Feces/microbiology ; },
abstract = {Osteoporosis is a complex metabolic bone disease that severely undermines the quality of life and overall health of the elderly. While previous studies have established a close relationship between gut microbiome and host bone metabolism, the role of genetic factors has received less scrutiny. This research aims to identify potential taxa associated with various bone mineral density states, incorporating assessments of genetic factors. Fecal microbiome profiles from 605 individuals (334 females and 271 males) aged 55-65 from the Taizhou Imaging Study with osteopenia (n = 270, 170 women) or osteoporosis (n = 94, 85 women) or normal (n = 241, 79 women) were determined using shotgun metagenomic sequencing. The linear discriminant analysis was employed to identify differentially enriched taxa. Utilizing the Kyoto Encyclopedia of Genes and Genomes for annotation, functional pathway analysis was conducted to identify differentially metabolic pathways. Polygenic risk score for osteoporosis was estimated to represent genetic susceptibility to osteoporosis, followed by stratification and interaction analyses. Gut flora diversity did not show significant differences among various bone mineral groups. After multivariable adjustment, certain species, such as Clostridium leptum, Fusicatenibacter saccharivorans and Roseburia hominis, were enriched in osteoporosis patients. Statistically significant interactions between the polygenic risk score and taxa Roseburia faecis, Megasphaera elsdenii were observed (P for interaction = 0.005, 0.018, respectively). Stratified analyses revealed a significantly negative association between Roseburia faecis and bone mineral density in the low-genetic-risk group (β = -0.045, P < 0.05), while Turicimonas muris was positively associated with bone mineral density in the high-genetic-risk group (β = 4.177, P < 0.05) after multivariable adjustments. Functional predictions of the gut microbiome indicated an increase in pathways related to structural proteins in high-genetic-risk patients, while low-genetic-risk patients exhibited enrichment in enzyme-related pathways. This study emphasizes the association between gut microbes and bone mass, offering new insights into the interaction between genetic background and gut microbiome.},
}
@article {pmid39178591,
year = {2024},
author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG},
title = {Unveiling the overlooked small-sized microbiome in river ecosystems.},
journal = {Water research},
volume = {265},
number = {},
pages = {122302},
doi = {10.1016/j.watres.2024.122302},
pmid = {39178591},
issn = {1879-2448},
mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; },
abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.},
}
@article {pmid39163656,
year = {2024},
author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q},
title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.},
journal = {Marine environmental research},
volume = {201},
number = {},
pages = {106694},
doi = {10.1016/j.marenvres.2024.106694},
pmid = {39163656},
issn = {1879-0291},
mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/enzymology ; Symbiosis ; Microbiota ; },
abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.},
}
@article {pmid39242535,
year = {2024},
author = {Attrah, M and Schärer, MR and Esposito, M and Gionchetta, G and Bürgmann, H and Lens, PNL and Fenner, K and van de Vossenberg, J and Robinson, SL},
title = {Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {164},
pmid = {39242535},
issn = {2049-2618},
support = {109070/WT_/Wellcome Trust/United Kingdom ; Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 200021L_201006//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Biofilms/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Rivers/microbiology ; *Metagenomics ; Microbiota/drug effects ; Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Planctomycetales/genetics/drug effects ; Metagenome ; Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.<br><br>RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.<br><br>CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.},
}
@article {pmid39239875,
year = {2024},
author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L},
title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2399260},
doi = {10.1080/19490976.2024.2399260},
pmid = {39239875},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; },
abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.},
}
@article {pmid39137550,
year = {2024},
author = {Gao, SM and Wang, P and Li, Q and Shu, WS and Tang, LY and Lin, ZL and Li, JT and Huang, LN},
title = {Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135478},
doi = {10.1016/j.jhazmat.2024.135478},
pmid = {39137550},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; *Mining ; *Microbiota ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; China ; Metagenomics ; Acids/metabolism ; Microbial Interactions ; },
abstract = {The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.},
}
@article {pmid39089643,
year = {2024},
author = {Gautam, J and Aggarwal, H and Kumari, D and Gupta, SK and Kumar, Y and Dikshit, M},
title = {A methionine-choline-deficient diet induces nonalcoholic steatohepatitis and alters the lipidome, metabolome, and gut microbiome profile in the C57BL/6J mouse.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1869},
number = {8},
pages = {159545},
doi = {10.1016/j.bbalip.2024.159545},
pmid = {39089643},
issn = {1879-2618},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/microbiology/etiology/pathology ; *Methionine/deficiency/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; Male ; *Metabolome ; Lipidomics ; Choline Deficiency/metabolism ; Liver/metabolism/pathology ; Choline/metabolism ; Lipid Metabolism ; Disease Models, Animal ; Diet/adverse effects ; },
abstract = {The methionine-choline-deficient (MCD) diet-induced non-alcoholic steatohepatitis (NASH) in mice is a well-established model. Our study aims to elucidate the factors influencing liver pathology in the MCD mouse model by examining physiological, biochemical, and molecular changes using histology, molecular techniques, and OMICS approaches (lipidomics, metabolomics, and metagenomics). Male C57BL/6J mice were fed a standard chow diet, a methionine-choline-sufficient (MCS) diet, or an MCD diet for 10 weeks. The MCD diet resulted in reduced body weight and fat mass, along with decreased plasma triglyceride, cholesterol, glucose, and insulin levels. However, it notably induced steatosis, inflammation, and alterations in gene expression associated with lipogenesis, inflammation, fibrosis, and the synthesis of apolipoproteins, sphingolipids, ceramides, and carboxylesterases. Lipid analysis revealed significant changes in plasma and tissues: most ceramide non-hydroxy-sphingosine lipids significantly decreased in the liver and plasma but increased in the adipose tissue of MCD diet-fed animals. Oxidized glycerophospholipids mostly increased in the liver but decreased in the adipose tissue of the MCD diet-fed group. The gut microbiome of the MCD diet-fed group showed an increase in Firmicutes and a decrease in Bacteroidetes and Actinobacteria. Metabolomic profiling demonstrated that the MCD diet significantly altered amino acid biosynthesis, metabolism, and nucleic acid metabolism pathways in plasma, liver, fecal, and cecal samples. LC-MS data indicated higher total plasma bile acid intensity and reduced fecal glycohyodeoxycholic acid intensity in the MCD diet group. This study demonstrates that although the MCD diet induces hepatic steatosis, the mechanisms underlying NASH in this model differ from those in human NASH pathology.},
}
@article {pmid39032544,
year = {2024},
author = {Ioannou, M and Borkent, J and Andreu-Sánchez, S and Wu, J and Fu, J and Sommer, IEC and Haarman, BCM},
title = {Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study.},
journal = {Brain, behavior, and immunity},
volume = {121},
number = {},
pages = {165-175},
doi = {10.1016/j.bbi.2024.07.009},
pmid = {39032544},
issn = {1090-2139},
mesh = {Humans ; *Schizophrenia/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Bipolar Disorder/microbiology ; Adult ; Middle Aged ; *Metagenome ; Metagenomics/methods ; Antipsychotic Agents/therapeutic use/pharmacology ; Bacteria/genetics ; },
abstract = {BACKGROUND: Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.<br><br>METHODS: In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n&#xa0;=&#xa0;203), including participants from a distinct population with a different metagenomic isolation protocol.<br><br>RESULTS: The gut microbiome of the patients had a significantly different &#x3b2;-diversity, but not &#x3b1;-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.<br><br>CONCLUSIONS: Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.},
}
@article {pmid39019160,
year = {2024},
author = {Zhu, Y and Yeo, EN and Smith, KM and Greenberg, AS and Rowan, S},
title = {Aging Modulates the Effect of Dietary Glycemic Index on Gut Microbiota Composition in Mice.},
journal = {The Journal of nutrition},
volume = {154},
number = {9},
pages = {2852-2861},
doi = {10.1016/j.tjnut.2024.07.014},
pmid = {39019160},
issn = {1541-6100},
mesh = {Animals ; Male ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; *Aging ; *Glycemic Index ; Mice ; *Diet ; *Feces/microbiology/chemistry ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Gut microbiome composition profoundly impacts host physiology and is modulated by several environmental factors, most prominently diet. The composition of gut microbiota changes over the lifespan, particularly during the earliest and latest stages. However, we know less about diet-aging interactions on the gut microbiome. We previously showed that diets with different glycemic indices, based on the ratio of rapidly digested amylopectin to slowly digested amylose, led to altered composition of gut microbiota in male C57BL/6J mice.<br><br>OBJECTIVES: Here, we examined the role of aging in influencing dietary effects on gut microbiota composition and aimed to identify gut bacterial taxa that respond to diet and aging.<br><br>METHODS: We studied 3 age groups of male C57BL/6J wild-type mice: young (4 mo), middle-aged (13.5 mo), and old (22 mo), all fed either high glycemic (HG) or low glycemic (LG) diets matched for caloric content and macronutrient composition. Fecal microbiome composition was determined by 16S rDNA metagenomic sequencing and was evaluated for changes in &#x3b1;- and &#x3b2;-diversity and bacterial taxa that change by age, diet, or both.<br><br>RESULTS: Young mice displayed lower &#x3b1;-diversity scores than middle-aged counterparts but exhibited more pronounced differences in &#x3b2;-diversity between diets. In contrast, old mice had slightly lower &#x3b1;-diversity scores than middle-aged mice, with significantly higher &#x3b2;-diversity distances. Within-group variance was lowest in young, LG-fed mice and highest in old, HG-fed mice. Differential abundance analysis revealed taxa associated with both aging and diet. Most differential taxa demonstrated significant interactions between diet and aging. Notably, several members of the Lachnospiraceae family increased with aging and HG diet, whereas taxa from the Bacteroides_H genus increased with the LG diet. Akkermansia muciniphila decreased with aging.<br><br>CONCLUSIONS: These findings illustrate the complex interplay between diet and aging in shaping the gut microbiota, potentially contributing to age-related disease.},
}
@article {pmid39237540,
year = {2024},
author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N},
title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7751},
pmid = {39237540},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Singapore ; Male ; Aged, 80 and over ; Female ; *Aging ; *Metagenome ; Asian People/genetics ; Phenotype ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; },
abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39232827,
year = {2024},
author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH},
title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {163},
pmid = {39232827},
issn = {2049-2618},
support = {2019YFA0905600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Face/microbiology ; Middle Aged ; *Skin Aging/physiology ; Female ; Adult ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Aging ; Metagenome ; Young Adult ; High-Throughput Nucleotide Sequencing ; Sebum/metabolism ; },
abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.<br><br>RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.<br><br>CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.},
}
@article {pmid39232089,
year = {2024},
author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G},
title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20545},
pmid = {39232089},
issn = {2045-2322},
mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation &amp; purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; },
abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.},
}
@article {pmid39230701,
year = {2024},
author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D},
title = {Metagenomic functional profiling: to sketch or not to sketch?.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_2},
pages = {ii165-ii173},
pmid = {39230701},
issn = {1367-4811},
support = {R01GM146462/GF/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; },
abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.<br><br>RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99&#xd7; faster in wall-clock time, and consumes up to 40-55&#xd7; less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.<br><br>This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.},
}
@article {pmid39143383,
year = {2024},
author = {Vijayan, J and Ezhuthanikkunnel, AP and Punnorkodu, SAK and Poikayil, SS and Mohan, M and Ammanamveetil, MHA},
title = {Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {39},
pages = {52132-52146},
pmid = {39143383},
issn = {1614-7499},
mesh = {*Geologic Sediments/microbiology ; *Estuaries ; India ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.},
}
@article {pmid39069433,
year = {2024},
author = {Tomiak, J and Stensvold, CR},
title = {Accelerating the paradigm shift in Blastocystis research.},
journal = {Trends in parasitology},
volume = {40},
number = {9},
pages = {775-776},
doi = {10.1016/j.pt.2024.07.006},
pmid = {39069433},
issn = {1471-5007},
mesh = {*Blastocystis/physiology ; *Blastocystis Infections/parasitology ; Humans ; Animals ; Gastrointestinal Microbiome/physiology ; },
abstract = {Blastocystis, once targeted as a harmful intestinal parasite, is now seen as potentially beneficial. Piperni et al. link its presence to improved gut health, higher microbial diversity, and favorable cardiometabolic outcomes, which suggests that Blastocystis might indicate a healthy diet and gut, possibly serving as a symbiont rather than a pathogen.},
}
@article {pmid39230075,
year = {2024},
author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I},
title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393791},
doi = {10.1080/19490976.2024.2393791},
pmid = {39230075},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; },
abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.},
}
@article {pmid39227168,
year = {2024},
author = {Salmaso, N and Cerasino, L and Pindo, M and Boscaini, A},
title = {Taxonomic and functional metagenomic assessment of a dolichospermum bloom in a large and deep lake south of the Alps.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae117},
pmid = {39227168},
issn = {1574-6941},
abstract = {Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome (MAG) obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.},
}
@article {pmid39089018,
year = {2024},
author = {Cui, M and Wang, M and Liu, X and Sun, H and Su, Z and Zheng, Y and Shen, Y and Wang, M},
title = {Mining and characterization of novel antimicrobial peptides from the large-scale microbiome of Shanxi aged vinegar based on metagenomics, molecular dynamics simulations and mechanism validation.},
journal = {Food chemistry},
volume = {460},
number = {Pt 2},
pages = {140646},
doi = {10.1016/j.foodchem.2024.140646},
pmid = {39089018},
issn = {1873-7072},
mesh = {*Metagenomics ; *Molecular Dynamics Simulation ; *Staphylococcus aureus/drug effects ; *Acetic Acid/chemistry/pharmacology ; *Escherichia coli/drug effects/genetics/metabolism ; Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics ; Anti-Bacterial Agents/pharmacology/chemistry ; Microbiota ; Microbial Sensitivity Tests ; Humans ; Lactobacillus/chemistry/metabolism ; },
abstract = {The study aimed to mine and characterize novel antimicrobial peptides (AMPs) from the Shanxi aged vinegar microbiome. Utilizing machine learning techniques, AlphaFold2 structure prediction and molecular dynamics simulations, six novel AMPs were innovatively mined from 98,539 peptides based on metagenomic data, of which one peptide secreted by Lactobacillus (named La-AMP) was experimentally validated to have remarkable bactericidal effects against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with high stability and no hemolytic activity. Scanning electron microscopy revealed that La-AMP caused irreversible damage to cell membranes of S. aureus and E. coli, a finding further confirmed by calcein-AM/propidium iodide staining. Additionally, La-AMP induced nucleic acid leakage and reactive oxygen species accumulation in bacterial cells. It was found to bind to DNA gyrase through salt bridges, hydrogen bonds, and hydrophobic interactions, ultimately inducing apoptosis. Thus, La-AMP exhibited encouraging promise as a valuable bioactive component for the development of natural preservatives.},
}
@article {pmid39222347,
year = {2024},
author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A},
title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001289},
pmid = {39222347},
issn = {2057-5858},
mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention &amp; control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.},
}
@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {410},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.},
}
@article {pmid39149810,
year = {2024},
author = {Liu, J and Wang, WJ and Xu, GF and Wang, YX and Lin, Y and Zheng, X and Yao, SH and Zheng, KH},
title = {Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (&gt;90 Years) and Elderly (65-74 Years) Adults.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {9},
pages = {461-469},
doi = {10.1089/omi.2024.0120},
pmid = {39149810},
issn = {1557-8100},
mesh = {Humans ; Aged ; *Longevity ; *Gastrointestinal Microbiome/physiology ; Aged, 80 and over ; Male ; Female ; China ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; East Asian People ; },
abstract = {The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.},
}
@article {pmid39145585,
year = {2024},
author = {Liu, B and Wang, G and Wang, L and Yan, J and Zhu, K and Liu, Q and Zhao, J and Jia, B and Fang, M and Rudich, Y and Morawska, L and Chen, J},
title = {Unraveling Cross-Organ Impacts of Airborne Pollutants: A Multiomics Study on Respiratory Exposure and Gastrointestinal Health.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {35},
pages = {15511-15521},
doi = {10.1021/acs.est.4c06035},
pmid = {39145585},
issn = {1520-5851},
mesh = {Mice ; Animals ; *Air Pollutants/toxicity ; Inhalation Exposure ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects ; Multiomics ; },
abstract = {Poor air quality is increasingly linked to gastrointestinal diseases, suggesting a potential correlation with human intestine health. However, this relationship remains largely unexplored due to limited research. This study used a controlled mouse model exposed to cooking oil fumes (COFs) and metagenomics, transcriptomics, and metabolomics to elucidate interactions between intestine microbiota and host metabolism under environmental stress. Our findings reveal that short-term COF inhalation induces pulmonary inflammation within 3 days and leads to gastrointestinal disturbances, elucidating a pathway connecting respiratory exposure to intestinal dysfunction. The exposure intensity significantly correlates with changes in intestinal tissue integrity, microbial composition, and metabolic function. Extended exposure of 7 days disrupts intestine microbiota and alters tryptophan metabolism, with further changes observed after 14 days, highlighting an adaptive response. These results highlight the vulnerability of intestinal health to airborne pollutants and suggest a pathway through which inhaled pollutants may affect distant organ systems.},
}
@article {pmid38977906,
year = {2024},
author = {Su, Q and Wong, OWH and Lu, W and Wan, Y and Zhang, L and Xu, W and Li, MKT and Liu, C and Cheung, CP and Ching, JYL and Cheong, PK and Leung, TF and Chan, S and Leung, P and Chan, FKL and Ng, SC},
title = {Multikingdom and functional gut microbiota markers for autism spectrum disorder.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2344-2355},
pmid = {38977906},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/diagnosis ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; *Feces/microbiology ; *Biomarkers/analysis ; Infant ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics/methods ; Machine Learning ; Archaea/genetics/metabolism/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Viruses/genetics/isolation &amp; purification/classification ; Metagenome ; },
abstract = {Associations between the gut microbiome and autism spectrum disorder (ASD) have been investigated although most studies have focused on the bacterial component of the microbiome. Whether gut archaea, fungi and viruses, or function of the gut microbiome, is altered in ASD is unclear. Here we performed metagenomic sequencing on faecal samples from 1,627 children (aged 1-13 years, 24.4% female) with or without ASD, with extensive phenotype data. Integrated analyses revealed that 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes and 12 metabolic pathways were altered in children with ASD. Machine learning using single-kingdom panels showed area under the curve (AUC) of 0.68 to 0.87 in differentiating children with ASD from those that are neurotypical. A panel of 31 multikingdom and functional markers showed a superior diagnostic accuracy with an AUC of 0.91, with comparable performance for males and females. Accuracy of the model was predominantly driven by the biosynthesis pathways of ubiquinol-7 or thiamine diphosphate, which were less abundant in children with ASD. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiota markers as non-invasive diagnostic tools in ASD.},
}
@article {pmid38141256,
year = {2024},
author = {Hassan-Zahraee, M and Ye, Z and Xi, L and Dushin, E and Lee, J and Romatowski, J and Leszczyszyn, J and Danese, S and Sandborn, WJ and Banfield, C and Gale, JD and Peeva, E and Longman, RS and Hyde, CL and Hung, KE},
title = {Baseline Serum and Stool Microbiome Biomarkers Predict Clinical Efficacy and Tissue Molecular Response After Ritlecitinib Induction Therapy in Ulcerative Colitis.},
journal = {Journal of Crohn's &amp; colitis},
volume = {18},
number = {9},
pages = {1361-1370},
doi = {10.1093/ecco-jcc/jjad213},
pmid = {38141256},
issn = {1876-4479},
support = {//Pfizer/ ; },
mesh = {Humans ; *Colitis, Ulcerative/drug therapy/blood/microbiology ; *Feces/microbiology/chemistry ; *Biomarkers/blood/analysis ; Male ; Female ; Adult ; Middle Aged ; Gastrointestinal Microbiome/drug effects ; Proteomics/methods ; Treatment Outcome ; Remission Induction ; Induction Chemotherapy/methods ; Metagenomics/methods ; },
abstract = {BACKGROUND AND AIMS: Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well-tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis [UC]. The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.<br><br>METHODS: Tissue and peripheral blood proteomics, transcriptomics, and faecal metagenomics were performed on samples before and after 8 weeks of oral ritlecitinib induction therapy [20 mg, 70 mg, 200 mg, or placebo once daily, N&#x2005;=&#x2005;39, 41, 33, and 18, respectively]. Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of faecal metagenomics was used to differentiate responders and nonresponders.<br><br>RESULTS: Peripheral blood serum proteomics identified four baseline serum markers [LTA, CCL21, HLA-E, MEGF10] predictive of modified clinical remission [MR], endoscopic improvement [EI], histological remission [HR], and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline [false discovery rate of <0.05]; of these, changes in four [IL4R, TNFRSF4, SPINK4, and LAIR-1] predicted concurrent EI and HR responses. Faecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.<br><br>CONCLUSIONS: Blood and microbiome biomarkers stratify endoscopic, histological, and tissue molecular responses to ritlecitinib, which may help guide future precision medicine approaches to UC treatment. ClinicalTrials.gov NCT02958865.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae424},
pmid = {39222062},
issn = {1477-4054},
support = {P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39218875,
year = {2024},
author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J},
title = {Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {346},
pmid = {39218875},
issn = {1741-7015},
mesh = {Humans ; Female ; Male ; *Transgender Persons ; Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Prospective Studies ; Metagenome ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts.<br><br>METHODS: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT.<br><br>RESULTS: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R[2]&#x2009;=&#x2009;4.1%, P&#x2009;=&#x2009;0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism.<br><br>CONCLUSIONS: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT02185274.},
}
@article {pmid39217389,
year = {2024},
author = {Zhang, Y and Cheng, TY and Liu, GH and Liu, L and Duan, DY},
title = {Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {370},
pmid = {39217389},
issn = {1756-3305},
support = {No. 31902294//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Sheep ; Cattle ; Female ; *Metagenome ; *Ixodidae/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification/genetics ; Tick Infestations/veterinary/parasitology ; Sheep Diseases/microbiology/parasitology ; China ; Metagenomics ; Tibet ; Cattle Diseases/microbiology/parasitology ; },
abstract = {BACKGROUND: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.<br><br>METHODS: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.<br><br>RESULTS: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.<br><br>CONCLUSIONS: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.},
}
@article {pmid39115410,
year = {2024},
author = {Moncada, C and Arnosti, C and Brüwer, JD and de Beer, D and Amann, R and Knittel, K},
title = {Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae159},
pmid = {39115410},
issn = {1751-7370},
support = {//Max Planck Society/ ; OCE-2022952//National Science Foundation/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/metabolism/isolation &amp; purification/genetics ; *Microbiota ; Svalbard ; Heterotrophic Processes ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.},
}
@article {pmid39098620,
year = {2024},
author = {Padasas-Adalla, CS and Ortega-Kindica, RCMH and Lomelí-Ortega, CO and Tabugo, SRM and Balcázar, JL},
title = {A metagenomics-based approach to decipher the resistome and mobilome of two seahorse species, Hippocampus barbouri and Hippocampus comes.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {3},
pages = {107296},
doi = {10.1016/j.ijantimicag.2024.107296},
pmid = {39098620},
issn = {1872-7913},
mesh = {Animals ; *Smegmamorpha/microbiology ; *Metagenomics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Skin/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbiota/genetics/drug effects ; Interspersed Repetitive Sequences/genetics ; },
abstract = {OBJECTIVE: This study aimed to explore the abundance and diversity of antibiotic resistance genes (ARGs) in seahorses (Hippocampus barbouri and Hippocampus comes) and their surrounding environment.<br><br>METHODS: A combination of shotgun metagenomics and bioinformatics was used to investigate the resistome of both seahorse species.<br><br>RESULTS: The analyses demonstrated a higher abundance of ARGs in seahorse-associated microbiomes, particularly in skin and gut samples, compared to those from water and sediment. Interestingly, genes conferring multidrug resistance (e.g., acrB, acrF, cpxA, msbA, and oqxB) were highly prevalent in all samples, especially in skin and gut samples. High levels of genes conferring resistance to fluoroquinolones (e.g., mfd and emrB), &#x3b2;-lactam (e.g., blaCMY-71, blaOXA-55, and penA), aminocoumarin (e.g., mdtB and mdtC), and peptide antibiotics (arnA, pmrE, and rosA) were also observed in skin and gut samples. An enrichment of mobile genetic elements (MGEs) was also observed in the analysed samples, highlighting their potential role in facilitating the acquisition and spread of ARGs. In fact, the abundance of mobilisation (MOB) relaxases (e.g., MOBF, MOBP, MOBT, and MOBV) in gut and skin samples suggests a high potential for conjugation events.<br><br>CONCLUSIONS: The occurrence of ARGs and MGEs in seahorses and the surrounding environment raises concerns about their transmission to humans, either through direct contact or the consumption of contaminated seafood. To the best of our knowledge, this study represents the first comprehensive analysis of ARGs in seahorse-associated microbiomes, and its results emphasise the need for monitoring and controlling the spread of ARGs in environmental settings.},
}
@article {pmid39096506,
year = {2024},
author = {Oggerin, M and Viver, T and Brüwer, J and Voß, D and García-Llorca, M and Zielinski, O and Orellana, LH and Fuchs, BM},
title = {Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39096506},
issn = {1751-7370},
support = {//Max Planck Society/ ; SO-245//UltraPac Expedition/ ; 03G0245A//Federal Ministry of Education and Research of Germany/ ; },
mesh = {*Seawater/microbiology ; Pacific Ocean ; Alphaproteobacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; In Situ Hybridization, Fluorescence ; Ecosystem ; Phylogeny ; Microbiota ; },
abstract = {One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.},
}
@article {pmid39043311,
year = {2024},
author = {Wang, X and Li, J and Wang, D and Sun, C and Zhang, X and Zhao, J and Teng, J and Wang, Q},
title = {Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124591},
doi = {10.1016/j.envpol.2024.124591},
pmid = {39043311},
issn = {1873-6424},
mesh = {*Geologic Sediments/chemistry/microbiology ; *Microplastics/toxicity ; *Nitrogen Cycle ; *Water Pollutants, Chemical/metabolism/analysis ; *Estuaries ; Metagenomics ; Nitrogen/metabolism ; Environmental Monitoring ; Microbiota/drug effects ; },
abstract = {Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.},
}
@article {pmid39019308,
year = {2024},
author = {Ewere, EE and White, S and Mauleon, R and Benkendorff, K},
title = {Soil microbial communities and degradation of pesticides in greenhouse effluent through a woodchip bioreactor.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124561},
doi = {10.1016/j.envpol.2024.124561},
pmid = {39019308},
issn = {1873-6424},
mesh = {*Bioreactors/microbiology ; *Soil Microbiology ; *Biodegradation, Environmental ; *Pesticides/metabolism/analysis ; Soil Pollutants/analysis/metabolism ; Microbiota ; Agriculture ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; },
abstract = {Pesticides, including insecticides and fungicides, are major contaminants in the effluent from intensive agricultural systems, such as greenhouses. Because of their constant use and persistence, some pesticides can accumulate in soil and/or run off into adjacent waterways. Microbial communities in soil can degrade some pesticides, and bioreactors with enhanced microbial communities have the potential to facilitate decontamination before the effluent is released into the environment. In this study, we sampled the soil along a gradient from immediately below greenhouses, into, through and below a bioreactor. Multi-analyte pesticide screening was undertaken along with shotgun metagenomic sequencing, to assess microbial community taxonomic profiles and metabolic pathway responses for functional analysis. Two insecticides (imidacloprid and fipronil) and nine fungicides were identified in the soil samples, with a general decrease in most pesticides with increasing distance from the greenhouses. Diversity indexes of taxonomic profiles show changes in the microbial community along the gradient. In particular, microbial communities were significantly different in the bioreactor, with lower Shannon diversity compared to immediately below the greenhouses, in the channels leading into the bioreactor and further downstream. Metabolic pathway analysis revealed significant changes in a wide range of core housekeeping genes such as protein/amino acid synthesis and lipid/fatty acid biosynthesis among the sampling sites. The result demonstrates that the composition and potential functional pathways of the microbial community shifted towards an increased tendency for phytol and contaminant degradation in the bioreactor, facilitated by high organic matter content. This highlights the potential to use enhanced microbial communities within bioreactors to reduce contamination by some pesticides in sediment receiving run-off from greenhouses.},
}
@article {pmid39014985,
year = {2024},
author = {Duggan DiDominic, KL and Shapleigh, JP and Walter, MT and Wang, YS and Reid, MC and Regan, JM},
title = {Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix.},
journal = {Journal of environmental quality},
volume = {53},
number = {5},
pages = {565-576},
doi = {10.1002/jeq2.20600},
pmid = {39014985},
issn = {1537-2537},
support = {1922551//National Science Foundation Research Traineeship (NRT) Program/ ; 2019-67019-29461//U.S. Department of Agriculture/ ; },
mesh = {*Bioreactors ; *Wood ; *Biofilms ; *Denitrification ; Microbiota ; Nitrogen/analysis ; Bacteria/genetics/metabolism ; },
abstract = {Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.},
}
@article {pmid38988320,
year = {2024},
author = {Kumar, M and Saini, HS},
title = {Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach.},
journal = {Journal of basic microbiology},
volume = {64},
number = {9},
pages = {e2400303},
doi = {10.1002/jobm.202400303},
pmid = {38988320},
issn = {1521-4028},
support = {//This study was funded by Department of Biotechnology (DBT), Ministry of Science and Technology, New Delhi (India) (Project number BT/PR7535/BCE/8/960/2013)./ ; },
mesh = {*Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Soil Microbiology ; *Metagenomics ; Wastewater/microbiology ; Phylogeny ; Biodiversity ; Proteobacteria/genetics/classification/metabolism/isolation &amp; purification ; DNA, Bacterial/genetics ; Metals, Heavy/metabolism/analysis ; Microbiota ; },
abstract = {Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.},
}
@article {pmid38936492,
year = {2024},
author = {Rodriguez-Ruiz, JP and Lin, Q and Van Heirstraeten, L and Lammens, C and Stewardson, AJ and Godycki-Cwirko, M and Coenen, S and Goossens, H and Harbarth, S and Malhotra-Kumar, S and , },
title = {Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {3},
pages = {107259},
doi = {10.1016/j.ijantimicag.2024.107259},
pmid = {38936492},
issn = {1872-7913},
mesh = {Humans ; *Ciprofloxacin/therapeutic use/pharmacology ; *Oropharynx/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome/drug effects/genetics ; *Urinary Tract Infections/microbiology/drug therapy ; Aged ; Adult ; Switzerland ; Belgium ; Poland ; Drug Resistance, Bacterial ; Feces/microbiology ; Microbiota/drug effects/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland.<br><br>METHODS: Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics.<br><br>RESULTS: At the end of therapy, patients treated with both short (&#x2264;7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, &#x3b2;-lactam, sulphonamide, and tetracycline resistance genes.<br><br>CONCLUSION: Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.},
}
@article {pmid39217229,
year = {2024},
author = {Gyaltshen, Y and Ishii, Y and Charvet, S and Goetz, E and Maruyama, S and Kim, E},
title = {Molecular diversity of green-colored microbial mats from hot springs of northern Japan.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {43},
pmid = {39217229},
issn = {1433-4909},
support = {KAKENHI 17H05713//Japan Society for the Promotion of Science/ ; 19H04713//Japan Society for the Promotion of Science/ ; CAREER 1453639//Division of Integrative Organismal Systems/ ; },
mesh = {*Hot Springs/microbiology ; Japan ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; },
abstract = {We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.},
}
@article {pmid39215001,
year = {2024},
author = {Becsei, &#xc1; and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P},
title = {Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7551},
pmid = {39215001},
issn = {2041-1723},
support = {NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Seasons ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Metagenome/genetics ; Europe ; },
abstract = {Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.},
}
@article {pmid39214983,
year = {2024},
author = {Duan, Y and Santos-Júnior, CD and Schmidt, TS and Fullam, A and de Almeida, BLS and Zhu, C and Kuhn, M and Zhao, XM and Bork, P and Coelho, LP},
title = {A catalog of small proteins from the global microbiome.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7563},
pmid = {39214983},
issn = {2041-1723},
support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Microbiota/genetics ; *Open Reading Frames/genetics ; *Bacteria/genetics/classification/metabolism ; *Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; Molecular Sequence Annotation ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.},
}
@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}
@article {pmid39209868,
year = {2024},
author = {Gonzalez, E and Lee, MD and Tierney, BT and Lipieta, N and Flores, P and Mishra, M and Beckett, L and Finkelstein, A and Mo, A and Walton, P and Karouia, F and Barker, R and Jansen, RJ and Green, SJ and Weging, S and Kelliher, J and Singh, NK and Bezdan, D and Galazska, J and Brereton, NJB},
title = {Spaceflight alters host-gut microbiota interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {71},
pmid = {39209868},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Space Flight ; Mice ; *Bacteria/classification/genetics ; Liver/microbiology ; Host Microbial Interactions ; Metagenomics/methods ; Colon/microbiology ; Bile Acids and Salts/metabolism ; Energy Metabolism ; Male ; Humans ; Mice, Inbred C57BL ; },
abstract = {The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.},
}
@article {pmid39209855,
year = {2024},
author = {Whittle, MJ and Castillo-Fernandez, J and Amos, GCA and Watson, P},
title = {Metagenomic characterisation of canine skin reveals a core healthy skin microbiome.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20104},
pmid = {39209855},
issn = {2045-2322},
mesh = {Dogs ; Animals ; *Skin/microbiology ; *Microbiota ; *Metagenomics/methods ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.},
}
@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}
@article {pmid39209850,
year = {2024},
author = {Colman, DR and Keller, LM and Arteaga-Pozo, E and Andrade-Barahona, E and St Clair, B and Shoemaker, A and Cox, A and Boyd, ES},
title = {Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7506},
pmid = {39209850},
issn = {2041-1723},
support = {80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {*Hot Springs/microbiology/chemistry ; *Metagenome ; *Phylogeny ; Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism ; Genome, Microbial ; Ecosystem ; Microbiota/genetics ; },
abstract = {The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.},
}
@article {pmid39206042,
year = {2024},
author = {Zhen, J and Zhang, Y and Li, Y and Zhou, Y and Cai, Y and Huang, G and Xu, A},
title = {The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1423662},
doi = {10.3389/fcimb.2024.1423662},
pmid = {39206042},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; *Carnosine/metabolism ; Male ; *Feces/microbiology ; Glucose Intolerance/metabolism ; Inflammation/metabolism ; Hep G2 Cells ; Metagenomics ; Female ; Middle Aged ; Taurochenodeoxycholic Acid/metabolism/pharmacology ; Hyperglycemia/metabolism ; Neutrophils/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/metabolism/genetics ; },
abstract = {OBJECTIVE: This study aims to investigate the pathogenesis of hyperglycemia and its associated vasculopathy using multiomics analyses in diabetes and impaired glucose tolerance, and validate the mechanism using the cell experiments.<br><br>METHODS: In this study, we conducted a comprehensive analysis of the metagenomic sequencing data of diabetes to explore the key genera related to its occurrence. Subsequently, participants diagnosed with impaired glucose tolerance (IGT), and healthy subjects, were recruited for fecal and blood sample collection. The dysbiosis of the gut microbiota (GM) and its associated metabolites were analyzed using 16S rDNA sequencing and liquid chromatograph mass spectrometry, respectively. The regulation of gene and protein expression was evaluated through mRNA sequencing and data-independent acquisition technology, respectively. The specific mechanism by which GM dysbiosis affects hyperglycemia and its related vasculopathy was investigated using real-time qPCR, Western blotting, and enzyme-linked immunosorbent assay techniques in HepG2 cells and neutrophils.<br><br>RESULTS: Based on the published data, the key alterable genera in the GM associated with diabetes were identified as Blautia, Lactobacillus, Bacteroides, Prevotella, Faecalibacterium, Bifidobacterium, Ruminococcus, Clostridium, and Lachnoclostridium. The related metabolic pathways were identified as cholate degradation and L-histidine biosynthesis. Noteworthy, Blautia and Faecalibacterium displayed similar alterations in patients with IGT compared to those observed in patients with diabetes, and the GM metabolites, tauroursodeoxycholic acid (TUDCA) and carnosine (CARN, a downstream metabolite of histidine and alanine) were both found to be decreased, which in turn regulated the expression of proteins in plasma and mRNAs in neutrophils. Subsequent experiments focused on insulin-like growth factor-binding protein 3 and interleukin-6 due to their impact on blood glucose regulation and associated vascular inflammation. Both proteins were found to be suppressed by TUDCA and CARN in HepG2 cells and neutrophils.<br><br>CONCLUSION: Dysbiosis of the GM occurred throughout the entire progression from IGT to diabetes, characterized by an increase in Blautia and a decrease in Faecalibacterium, leading to reduced levels of TUDCA and CARN, which alleviated their inhibition on the expression of insulin-like growth factor-binding protein 3 and interleukin-6, contributing to the development of hyperglycemia and associated vasculopathy.},
}
@article {pmid39205200,
year = {2024},
author = {Santos, JPN and Rodrigues, GVP and Ferreira, LYM and Monteiro, GP and Fonseca, PLC and Lopes, &#xcd;S and Florêncio, BS and da Silva Junior, AB and Ambrósio, PE and Pirovani, CP and Aguiar, ERGR},
title = {The Virome of Cocoa Fermentation-Associated Microorganisms.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/v16081226},
pmid = {39205200},
issn = {1999-4915},
support = {Financial code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brazil (CAPES)/ ; Researcher fellowship//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; },
mesh = {*Cacao/virology/microbiology ; *Fermentation ; *Virome ; Viruses/genetics/classification/isolation &amp; purification ; Fungi/virology/genetics/classification ; Phylogeny ; Bacteriophages/genetics/classification/isolation &amp; purification ; Costa Rica ; Bacteria/genetics/classification/virology ; Metagenomics ; Genome, Viral ; },
abstract = {Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.},
}
@article {pmid39202331,
year = {2024},
author = {Zheng, X and Xu, L and Tang, Q and Shi, K and Wang, Z and Shi, L and Ding, Y and Yin, Z and Zhang, X},
title = {Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/genes15080970},
pmid = {39202331},
issn = {2073-4425},
support = {202103a06020013//Major special science and technology project of Anhui Province/ ; GXXT-2023-059//the Cooperative Innovation Project of Anhui Provincial Universities/ ; 340000211260001000431//the Joint Research Project on Local Pig Breeding in Anhui Province/ ; 2021YFD1301200//National Key research and development Program of China/ ; },
mesh = {Animals ; *Weaning ; *Gastrointestinal Microbiome ; Swine ; *Metabolomics/methods ; *Metagenomics/methods ; Stress, Physiological ; Metabolome ; Animals, Newborn ; Cecum/microbiology/metabolism ; },
abstract = {(1) Background: Weaning is a challenging and stressful event in the pig's life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&amp;E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student's t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses-350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages.},
}
@article {pmid39201270,
year = {2024},
author = {Su, H and Yang, S and Chen, S and Chen, X and Guo, M and Zhu, L and Xu, W and Liu, H},
title = {What Happens in the Gut during the Formation of Neonatal Jaundice-Underhand Manipulation of Gut Microbiota?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168582},
pmid = {39201270},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Jaundice, Neonatal/therapy/microbiology/etiology ; Infant, Newborn ; *Probiotics ; *Bilirubin/metabolism/blood ; Breast Feeding ; Milk, Human/microbiology/metabolism ; },
abstract = {Jaundice is a symptom of high blood bilirubin levels affecting about 80% of neonates. In neonates fed with breast milk, jaundice is particularly prevalent and severe, which is likely multifactorial. With the development of genomics and metagenomics, a deeper understanding of the neonatal gut microbiota has been achieved. We find there are accumulating evidence to indicate the importance of the gut microbiota in the mechanism of jaundice. In this paper, we present new comprehensive insight into the relationship between the microbiota and jaundice. In the new perspective, the gut is a crucial crossroad of bilirubin excretion, and bacteria colonizing the gut could play different roles in the excretion of bilirubin, including Escherichia coli as the main traffic jam causers, some Clostridium and Bacteroides strains as the traffic police, and most probiotic Bifidobacterium and Lactobacillus strains as bystanders with no effect or only a secondary indirect effect on the metabolism of bilirubin. This insight could explain why breast milk jaundice causes a longer duration of blood bilirubin and why most probiotics have limited effects on neonatal jaundice. With the encouragement of breastmilk feeding, our perspective could guide the development of new therapy methods to prevent this side effect of breastfeeding.},
}
@article {pmid39201260,
year = {2024},
author = {Ryu, HM and Islam, SMS and Riaz, B and Sayeed, HM and Choi, B and Sohn, S},
title = {Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168571},
pmid = {39201260},
issn = {1422-0067},
mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Colitis/microbiology/therapy/diet therapy/chemically induced ; *Dextran Sulfate/toxicity ; RNA, Ribosomal, 16S/genetics ; Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy ; Biomarkers ; Mice, Inbred C57BL ; Colon/microbiology/pathology/metabolism ; },
abstract = {Ulcerative colitis (UC) is a persistent inflammatory intestinal disease that consistently affects the colon and rectum. Its exact cause remains unknown. UC causes a considerable challenge in healthcare, prompting research for novel therapeutic strategies. Although probiotics have gained popularity as possible candidates for managing UC, studies are still ongoing to identify the best probiotics or probiotic mixtures for clinical applications. This study aimed to determine the efficacy of a multi-strain probiotic mixture in mitigating intestinal inflammation in a colitis mouse model induced by dextran sulfate sodium. Specifically, a multi-strain probiotic mixture consisting of Tetragenococcus halophilus and Eubacterium rectale was used to study its impact on colitis symptoms. Anti-inflammatory effects were evaluated using ELISA and flow cytometry. The configuration of gut microbial communities was determined using 16S rRNA metagenomic analysis. According to this study, colitis mice treated with the probiotic mixture experienced reduced weight loss and significantly less colonic shortening compared to untreated mice. Additionally, the treated mice exhibited increased levels of forkhead box P3 (Foxp3) and interleukin 10, along with decreased expression of dendritic cell activation markers, such as CD40+, CD80+, and CD83+, in peripheral blood leukocytes and intraepithelial lymphocytes. Furthermore, there was a significant decrease in the frequencies of CD8+N.K1.1+ cells and CD11b+Ly6G+ cells. In terms of the gut microbiota, probiotic-mixture treatment of colitis mice significantly increased the abundance of the phyla Actinobacteria and Verrucomicrobia (p < 0.05). These results provide valuable insights into the therapeutic promise of multi-strain probiotics, shedding light on their potential to alleviate colitis symptoms. This research contributes to the ongoing exploration of effective probiotic interventions for managing inflammatory bowel disease.},
}
@article {pmid39201258,
year = {2024},
author = {Al-Sarraj, F and Albiheyri, R and Qari, M and Alotaibi, M and Al-Zahrani, M and Anwar, Y and Alghamdi, MA and Nass, NM and Bouback, T and Alotibi, I and Radhwi, O and Sajer, BH and Redhwan, A and Al-Matary, MA and Almanzalawi, EA and Elshafie, HS},
title = {Genetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168570},
pmid = {39201258},
issn = {1422-0067},
support = {grant no. J: 007-130-1443.//Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah/ ; },
mesh = {Humans ; *Anemia, Sickle Cell/microbiology/genetics ; *Mouth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; Case-Control Studies ; Adolescent ; High-Throughput Nucleotide Sequencing ; Middle Aged ; },
abstract = {The Middle Eastern prevalence of sickle cell anemia, a genetic disorder that affects red blood cells, necessitates additional research. On a molecular level, we sought to identify and sort the oral microbiota of healthy individuals and those with sickle cell anemia. Furthermore, it is crucial to comprehend how changes in the genetic makeup of the oral microbiota impact the state of sickle cell anemia. Using next-generation sequencing, the 16S rRNA amplicon was examined using saliva samples from 36 individuals with sickle cell anemia and healthy individuals. These samples were obtained from sickle cell anemia patients (18 samples) and healthy control participants (controls, 18 samples). Various analyses are conducted using bioinformatic techniques to identify distinct species and their relative abundance. Streptococcus, followed by Fusobacterium nucleatum, Prevotella, and Veillonella were the most prevalent genera of bacteria in the saliva of the SCA and non-SCA individuals according to our findings. Rothia mucilaginosa, Prevotella scoposa, and Veillonella dispar species were the dominant species in both sickle cell anemia and non-sickle cell anemia subjects. Streptococcus salivarius, Actinomyces graevenitzii, Actinomyces odontolyticus, and Actinomyces georgiae spp. were the most prevalent bacterial spp. in the studied SCA cases. The sequencing of the 16S rRNA gene yielded relative abundance values that were visualized through a heatmap analysis. Alterations in the oral microflora's constitution can significantly affect the susceptibility of sickle cell anemia patients to develop more severe health complications. Salivary diagnosis is a potential tool for predicting and preventing oral microbiome-related diseases in the future.},
}
@article {pmid39197040,
year = {2024},
author = {Chen, S and Zhang, Z and Liu, S and Chen, T and Lu, Z and Zhao, W and Mou, X and Liu, S},
title = {Consistent signatures in the human gut microbiome of longevous populations.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393756},
pmid = {39197040},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Longevity ; Aged, 80 and over ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Female ; Adult ; Male ; Aged ; Young Adult ; Metagenomics ; Middle Aged ; Desulfovibrio/genetics/metabolism ; },
abstract = {Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.},
}
@article {pmid39198832,
year = {2024},
author = {Su, W and Gong, C and Zhong, H and Yang, H and Chen, Y and Wu, X and Jin, J and Xi, H and Zhao, J},
title = {Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes.},
journal = {Reproductive biology and endocrinology : RB&amp;E},
volume = {22},
number = {1},
pages = {111},
pmid = {39198832},
issn = {1477-7827},
support = {437606312//Wenzhou Medical University advantageous and distinctive Discipline Construction Project/ ; },
mesh = {Humans ; Female ; *Embryo Transfer/methods ; *Dysbiosis/microbiology ; Adult ; *Vagina/microbiology ; *Microbiota/genetics/physiology ; *Endometrium/microbiology/metabolism ; *Embryo Implantation/physiology ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.<br><br>PURPOSE: This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.<br><br>METHODS: We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.<br><br>RESULTS: Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC&#x2009;=&#x2009;0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.<br><br>CONCLUSIONS: This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.},
}
@article {pmid39198826,
year = {2024},
author = {Su, Q and Zhuang, DH and Li, YC and Chen, Y and Wang, XY and Ge, MX and Xue, TY and Zhang, QY and Liu, XY and Yin, FQ and Han, YM and Gao, ZL and Zhao, L and Li, YX and Lv, MJ and Yang, LQ and Xia, TR and Luo, YJ and Zhang, Z and Kong, QP},
title = {Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {232},
pmid = {39198826},
issn = {1474-760X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Acclimatization ; *Altitude ; Animals ; Adult ; Male ; *Hypoxia/genetics ; Mice ; Female ; Longitudinal Studies ; Altitude Sickness/microbiology/genetics ; Middle Aged ; },
abstract = {BACKGROUND: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization.<br><br>RESULTS: To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress.<br><br>CONCLUSIONS: Our study underscores the importance of Blautia A species in the gut microbiota's rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.},
}
@article {pmid39198450,
year = {2024},
author = {Licht, P and Dominelli, N and Kleemann, J and Pastore, S and Müller, ES and Haist, M and Hartmann, KS and Stege, H and Bros, M and Meissner, M and Grabbe, S and Heermann, R and Mailänder, V},
title = {The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {74},
pmid = {39198450},
issn = {2055-5008},
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; Female ; Middle Aged ; Male ; *Staphylococcus aureus/genetics/pathogenicity/isolation &amp; purification ; *Lymphoma, T-Cell, Cutaneous/microbiology ; Aged ; *Mycosis Fungoides/microbiology ; Dysbiosis/microbiology ; Skin Neoplasms/microbiology/pathology ; Adult ; Aged, 80 and over ; Metagenomics/methods ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.},
}
@article {pmid39198444,
year = {2024},
author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J},
title = {Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7447},
pmid = {39198444},
issn = {2041-1723},
support = {UL1TR002377//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Feces/microbiology ; *Health Status ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; },
abstract = {Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.},
}
@article {pmid39198442,
year = {2024},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7450},
pmid = {39198442},
issn = {2041-1723},
support = {192514//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Feces/microbiology ; *Escherichia coli/genetics/isolation &amp; purification ; Humans ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Nanopores ; Escherichia coli Proteins/genetics ; Plasmids/genetics ; Nanopore Sequencing/methods ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; },
abstract = {The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.},
}
@article {pmid39198293,
year = {2024},
author = {Joseph, B and Babu, S},
title = {Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {331},
pmid = {39198293},
issn = {1432-0991},
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Helianthus/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Plant Leaves/microbiology ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Manure/microbiology ; Microbiota ; Biodiversity ; Metagenomics ; },
abstract = {Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.},
}
@article {pmid39127317,
year = {2024},
author = {Tang, W and Wang, Q and Sun, M and Liu, C and Huang, Y and Zhou, M and Zhang, X and Meng, Z and Zhang, J},
title = {The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders.},
journal = {Life sciences},
volume = {354},
number = {},
pages = {122952},
doi = {10.1016/j.lfs.2024.122952},
pmid = {39127317},
issn = {1879-0631},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Oligodendroglia/metabolism ; *Homeostasis/physiology ; *Demyelinating Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Myelin Sheath/metabolism ; },
abstract = {The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.},
}
@article {pmid39110597,
year = {2024},
author = {Fu, Y and Yu, S and Li, J and Lao, Z and Yang, X and Lin, Z},
title = {DeepMineLys: Deep mining of phage lysins from human microbiome.},
journal = {Cell reports},
volume = {43},
number = {8},
pages = {114583},
doi = {10.1016/j.celrep.2024.114583},
pmid = {39110597},
issn = {2211-1247},
mesh = {Humans ; *Microbiota ; *Bacteriophages/genetics/metabolism ; Data Mining ; Viral Proteins/metabolism ; Neural Networks, Computer ; Animals ; Muramidase/metabolism ; Escherichia coli/genetics/metabolism ; },
abstract = {Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.},
}
@article {pmid38986824,
year = {2024},
author = {de Deus, DR and Siqueira, JAM and Maués, MAC and de Fátima Mesquita de Figueiredo, MJ and Júnior, ECS and da Silva Bandeira, R and da Costa Pinheiro, K and Teixeira, DM and da Silva, LD and de Fátima Dos Santos Guerra, S and da Silva Soares, L and Gabbay, YB},
title = {Analysis of viral diversity in dogs with acute gastroenteritis from Brazilian Amazon.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {123},
number = {},
pages = {105637},
doi = {10.1016/j.meegid.2024.105637},
pmid = {38986824},
issn = {1567-7257},
mesh = {Dogs ; Animals ; *Gastroenteritis/virology/veterinary/epidemiology ; Brazil/epidemiology ; *Dog Diseases/virology/epidemiology ; *Phylogeny ; Norovirus/genetics/classification/isolation &amp; purification ; Feces/virology ; Genome, Viral ; Genetic Variation ; Metagenomics/methods ; Viruses/classification/genetics/isolation &amp; purification ; Virome ; },
abstract = {Viral gastroenteritis is commonly reported in dogs and involves a great diversity of enteric viruses. In this research, viral diversity was investigated in dogs with diarrhea in Northern Brazil using shotgun metagenomics. Furthermore, the presence of norovirus (NoV) was investigated in 282 stool/rectal swabs of young/adult dogs with or without diarrhea from two public kennels, based on one-step reverse transcription polymerase chain reaction (RT-PCR) for genogroup VI and VII (GVI and GVII) and real-time RT-PCR for GI, GII, and GIV. Thirty-one viral families were identified, including bacteriophages. Phylogenetic analyses showed twelve complete or nearly complete genomes belonging to the species of Protoparvovirus carnivoran1, Mamastrovirus 5, Aichivirus A2, Alphacoronavirus 1, and Chipapillomavirus 1. This is the first description of the intestinal virome of dogs in Northern Brazil and the first detection of canine norovirus GVII in the country. These results are important for helping to understand the viral groups that circulate in the canine population.},
}
@article {pmid38964747,
year = {2024},
author = {Łukasik, J and Dierikx, T and Johnston, BC and de Meij, T and Szajewska, H},
title = {Systematic review: effect of probiotics on antibiotic-induced microbiome disruption.},
journal = {Beneficial microbes},
volume = {15},
number = {5},
pages = {431-447},
doi = {10.1163/18762891-bja00023},
pmid = {38964747},
issn = {1876-2891},
mesh = {*Probiotics/pharmacology/administration &amp; dosage ; Humans ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Dysbiosis/microbiology ; Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effectiveness of probiotics in preventing or reversing antibiotic-induced microbiome disruption remains uncertain, and claims of microbiome restoration to its pre-antibiotic state may be overestimated. In this review, we aimed to assess the efficacy of probiotics in preventing or ameliorating disruptions in microbiome composition and function induced by antibiotic treatment. We searched Medline, Embase, and CENTRAL for randomised controlled and non-randomised trials. Participants were individuals of any age who were on systemic antibiotics with a low risk of baseline dysbiosis. The intervention consisted of probiotics during or after antibiotic treatment, compared to placebo, alternative interventions, or no intervention. Outcomes included microbiome composition and diversity analysed using high-throughput molecular methods, alongside microbial function and resistome assessments. Seven studies, reported in eight papers, were reviewed. One study showed probiotics counteracting antibiotic-induced diversity changes, another showed exacerbation of these changes, and four others showed no effect. Effects on taxa abundance ranged from mitigating dysbiosis to selective modulation, no effect, or delayed recovery. One study observed no impact on the resistome, while another reported an increase in antibiotic resistance genes. In conclusion, heterogeneous results preclude a definitive conclusion on the effectiveness of any specific probiotic in restoring antibiotic-exposed microbiomes. For a clearer understanding, future research should be more standardised and long-term, employing advanced methods, such as 16S rRNA gene sequencing and metagenomic sequencing. These studies should strive to include larger, diverse populations to enhance generalisability and clearly define what constitutes a healthy microbiome. Finally, linking changes in the microbiome to specific clinical outcomes is essential for clinical decision making. PROSPERO registration number: CRD42023446214.},
}
@article {pmid38960356,
year = {2024},
author = {Zhang, W and Ye, J and Hu, F and Zhang, J and Chen, P and Yuan, Z and Xu, Z},
title = {Microbial community succession and responses to internal environmental drivers throughout the operation of constructed wetlands.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119522},
doi = {10.1016/j.envres.2024.119522},
pmid = {38960356},
issn = {1096-0953},
mesh = {*Wetlands ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; },
abstract = {Constructed wetlands (CWs) have been widely used to ensure effective domestic wastewater treatment. Microorganisms-derived CWs have received extensive attention as they play a crucial role. However, research on the succession patterns of microbial communities and the influencing mechanisms of internal environmental factors throughout entire CW operations remains limited. In this context, three parallel-operated CWs were established in this study to assess the microbial communities and their influencing environmental factors at different substrate depths throughout the operation process using 16S rRNA gene high-throughput sequencing and metagenomic sequencing. The results showed gradual reproduction and accumulation of the microbial communities throughout the CW operation. Although gradual increases in the richness and diversity of the microbial communities were found, there were decreases in the functional expression of the dominant microbial species. The excessive accumulation of microorganisms will decrease the oxidation-reduction potential (ORP) within CWs and attenuate their influence on effluent. Dissolved oxygen (DO) was the major factor influencing the microbial community succession over the CW operation. The main identified functional bacterial genera responsible for the ammonium oxidation, nitrification, and denitrification processes in the CWs were Nitrosospira, Nitrobacter, Nitrospira, Rhodanobacter, and Nakamurella. The narG gene was identified as a key functional gene linking various components of nitrogen cycling, while pH, electrical conductivity (EC), and ORP were the major environmental factors affecting the metabolism characteristics of nitrogen functional microorganisms. This study provides a theoretical basis for the effective regulation of related microbial communities to achieve long-term, efficient, and stable CW operations.},
}
@article {pmid39195462,
year = {2024},
author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y},
title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.},
journal = {Marine drugs},
volume = {22},
number = {8},
pages = {},
doi = {10.3390/md22080346},
pmid = {39195462},
issn = {1660-3397},
support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; },
mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; },
abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.},
}
@article {pmid39192682,
year = {2024},
author = {Flynn, PJ and Moreau, CS},
title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17519},
doi = {10.1111/mec.17519},
pmid = {39192682},
issn = {1365-294X},
support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; },
abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.},
}
@article {pmid39192352,
year = {2024},
author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L},
title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.},
journal = {Hereditas},
volume = {161},
number = {1},
pages = {26},
pmid = {39192352},
issn = {1601-5223},
support = {No. 2023349//Chengdu Municipal Health Commission/ ; },
mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.<br><br>METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.<br><br>RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.<br><br>CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.},
}
@article {pmid39192220,
year = {2024},
author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S},
title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {315},
pmid = {39192220},
issn = {1471-2180},
support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; },
mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.},
}
@article {pmid39191812,
year = {2024},
author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H},
title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {72},
pmid = {39191812},
issn = {2055-5008},
mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; },
abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.},
}
@article {pmid39191760,
year = {2024},
author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R},
title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {73},
pmid = {39191760},
issn = {2055-5008},
support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.},
}
@article {pmid39189742,
year = {2024},
author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C},
title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.},
journal = {mBio},
volume = {},
number = {},
pages = {e0204424},
doi = {10.1128/mbio.02044-24},
pmid = {39189742},
issn = {2150-7511},
abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.},
}
@article {pmid39113195,
year = {2024},
author = {Dong, T and Wang, Y and Qi, C and Fan, W and Xie, J and Chen, H and Zhou, H and Han, X},
title = {Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {8},
pages = {1617-1626},
doi = {10.4014/jmb.2402.02004},
pmid = {39113195},
issn = {1738-8872},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Microbiota/genetics/drug effects ; Retrospective Studies ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests ; Respiratory Tract Infections/microbiology/drug therapy ; Genes, Bacterial/genetics ; Male ; Female ; Middle Aged ; },
abstract = {Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.},
}
@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {34},
number = {9},
pages = {3420-3433},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; R35GM133510/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Feces/microbiology ; Pilot Projects ; Male ; Female ; Cross-Sectional Studies ; Case-Control Studies ; Middle Aged ; *Bariatric Surgery ; *Bile Acids and Salts/metabolism ; Adult ; *Obesity, Morbid/surgery/microbiology ; Gastrointestinal Microbiome/physiology ; Weight Loss ; Lithocholic Acid/metabolism ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.<br><br>METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1&#xa0;months post-BRS.&#xa0;We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.<br><br>RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p&#x2009;=&#x2009;0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p&#x2009;<&#x2009;0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of&#x2009;-&#x2009;3.32 and&#x2009;-&#x2009;2.64, respectively, adjusted p&#x2009;<&#x2009;0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.<br><br>CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}
@article {pmid38807549,
year = {2024},
author = {Bae, WY and Jung, WH and Shin, SL and Kim, TR and Sohn, M and Suk, J and Jung, I and Lee, YI and Lee, JH},
title = {Heat-treated Limosilactobacillus fermentum LM1020 with menthol, salicylic acid, and panthenol promotes hair growth and regulates hair scalp microbiome balance in androgenetic alopecia: A double-blind, randomized and placebo-controlled clinical trial.},
journal = {Journal of cosmetic dermatology},
volume = {23},
number = {9},
pages = {2943-2955},
doi = {10.1111/jocd.16357},
pmid = {38807549},
issn = {1473-2165},
support = {S3003957//Ministry of SMEs and Startups/ ; },
mesh = {Humans ; *Alopecia/therapy/microbiology/drug therapy ; Double-Blind Method ; *Scalp/microbiology ; *Microbiota/drug effects ; Adult ; *Limosilactobacillus fermentum/physiology/isolation &amp; purification ; Male ; Female ; Hair/microbiology/growth &amp; development ; Middle Aged ; Hair Follicle/microbiology ; Hot Temperature ; Cell Proliferation/drug effects ; },
abstract = {BACKGROUND: Androgenetic alopecia (AGA) is a common and chronic problem characterized by hair follicle miniaturization.<br><br>AIMS: In this study, heat-treated Limosilactobacillus fermentum LM1020 (HT-LM1020) was investigated in human follicle dermal papilla cell (HFDPC), scalp tissue, and clinical trials for patients with AGA.<br><br>PATIENTS/METHODS: Cell proliferation and the expression of cyclins and cyclin-dependent kinases (CDKs) were measured in HFDPC. The relative gene expression of 5&#x3b1;-reductase and growth factors were investigated in hair scalp. This double-blind, randomized, placebo-controlled clinical trial was conducted over 24&#x2009;weeks. Primary efficacy was evaluated by measuring hair density, and secondary efficacy was assessed by experts and self-assessment. Changes in the microbiota of the hair scalps were analyzed using 16S metagenome amplicon sequencing.<br><br>RESULTS: HT-LM1020 promoted cell growth (p&#x2009;<&#x2009;0.001) and cyclin B1 expression, and it reduced 5&#x3b1;-reductase and induced fibroblast growth factor 7 (FGF7), FGF10, and epithelial growth factor7 (EGF7) (p&#x2009;<&#x2009;0.001). In the clinical trial, the experimental group demonstrated an increase in hair density from 133.70 to 148.87&#x2009;n/cm[2] at Week 24 (p&#x2009;<&#x2009;0.001), while also expressing satisfaction with their hair density, reduced hair loss, and hairline. At Week 24, the total ratio of lactic acid bacteria operational taxonomic unit (OTU) in the scalp increased from 6.65% to 26.19%. At the same period, placebo-controlled group decreased Staphylococcus caprae OTU from 77.95% to 14.57% while experimental group decreased from 65.80% to 41.02%.<br><br>CONCLUSIONS: These present results showed that HT-LM1020 was a co-effector of ingredients for anti-hair loss contributing to cell proliferation and the expression of CDKs.},
}
@article {pmid39189169,
year = {2024},
author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD},
title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.},
journal = {Journal of xenobiotics},
volume = {14},
number = {3},
pages = {970-988},
doi = {10.3390/jox14030054},
pmid = {39189169},
issn = {2039-4713},
support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.},
}
@article {pmid39187802,
year = {2024},
author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH},
title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1001},
pmid = {39187802},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation &amp; purification ; Aged ; },
abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.<br><br>METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).<br><br>RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.<br><br>CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.<br><br>TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.},
}
@article {pmid39185682,
year = {2024},
author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES},
title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2394248},
doi = {10.1080/19490976.2024.2394248},
pmid = {39185682},
issn = {1949-0984},
mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation &amp; purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation &amp; purification/genetics ; Longitudinal Studies ; },
abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.},
}
@article {pmid39120615,
year = {2024},
author = {Li, X and Tao, Q and Hu, Q and Ma, N and Ma, G},
title = {In vitro gastrointestinal digestion and fecal fermentation of Pleurotus eryngii proteins extracted using different methods: insights for the utilization of edible mushroom-based proteins as novel nutritional and functional components.},
journal = {Food &amp; function},
volume = {15},
number = {17},
pages = {8865-8877},
doi = {10.1039/d4fo02604g},
pmid = {39120615},
issn = {2042-650X},
mesh = {*Pleurotus/metabolism/chemistry ; *Digestion ; *Fermentation ; *Feces/microbiology ; *Fungal Proteins/metabolism ; Humans ; Gastrointestinal Tract/metabolism/microbiology ; Gastrointestinal Microbiome ; Hydrolysis ; },
abstract = {Pleurotus eryngii (P. eryngii) protein is considered a high-quality protein because it is rich in essential amino acids and displays multiple significant functional characterizations that vary with its fabrication processes. We aimed to investigate the differences in P. eryngii protein extracted via alkaline extraction and acid precipitation (AA), cellulase complex alkaline extraction and acid precipitation (CAA), ultrasound-assisted alkaline extraction and acid precipitation (UAA), and salt dissolution (S) in terms of gastrointestinal digestion and fecal fermentation consequences. Protein hydrolysis and structural analysis were performed after in vitro gastrointestinal digestion, and it was found that AA showed the highest hydrolysis degree, whereas CAA showed the lowest. The results of fluorescence chromatography and infrared chromatography indicated that the reasons for the digestion difference might be the unfolding degrees of the protein tertiary structure and polysaccharide content, which is the major component of crude proteins and can prevent protein hydrolysis. Metagenomic analysis suggested that compared with other groups, AA had excellent biological functions, including regulating obesity and insulin-related microbiota. This study could provide a new theoretical basis for the P. eryngii protein as a novel type of nutritional and functional component and contributes to the development of a diversified emerging food protein supply system.},
}
@article {pmid39117202,
year = {2024},
author = {Tariq, M and Liu, Y and Rizwan, A and Shoukat, CA and Aftab, Q and Lu, J and Zhang, Y},
title = {Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175354},
doi = {10.1016/j.scitotenv.2024.175354},
pmid = {39117202},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Nitrogen/metabolism ; *Carbon Dioxide/metabolism ; *Microbiota ; *Carbon/metabolism ; Climate Change ; Soil/chemistry ; Carbon Cycle ; },
abstract = {In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.},
}
@article {pmid39111416,
year = {2024},
author = {Wang, HY and Yu, ZG and Zhou, FW and Hernandez, JC and Grandjean, A and Biester, H and Xiao, KQ and Knorr, KH},
title = {Microbial communities and functions are structured by vertical geochemical zones in a northern peatland.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175273},
doi = {10.1016/j.scitotenv.2024.175273},
pmid = {39111416},
issn = {1879-1026},
mesh = {*Microbiota ; China ; *Soil Microbiology ; *Methane/metabolism/analysis ; RNA, Ribosomal, 16S ; Soil/chemistry ; Wetlands ; Carbon/analysis ; Nitrogen/analysis ; Bacteria/classification ; Sulfur/metabolism/analysis ; Archaea/classification ; },
abstract = {Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L[-1]. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm[-3]·d[-1], while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.},
}
@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}
@article {pmid39082382,
year = {2024},
author = {Vidal-Villarejo, M and Dößelmann, B and Kogler, B and Hammerschmidt, M and Oppliger, B and Oppliger, H and Schmid, K},
title = {Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis.},
journal = {Molecular ecology},
volume = {33},
number = {17},
pages = {e17482},
doi = {10.1111/mec.17482},
pmid = {39082382},
issn = {1365-294X},
support = {SCHM 1354-11/1//Deutsche Forschungsgemeinschaft/ ; 031B0731A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; PGRL-NN-0061//Swiss National Action Plan NAP-PGREL/ ; },
mesh = {*Zea mays/microbiology ; Switzerland ; *Ascomycota/genetics ; *Plant Leaves/microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; *Metagenomics ; },
abstract = {The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.},
}
@article {pmid39056112,
year = {2024},
author = {Dong, J and Zhang, J and Cheng, S and Qin, B and Jin, K and Chen, B and Zhang, Y and Lu, J},
title = {A high-fat diet induced depression-like phenotype via hypocretin-HCRTR1 mediated inflammation activation.},
journal = {Food &amp; function},
volume = {15},
number = {17},
pages = {8661-8673},
doi = {10.1039/d4fo00210e},
pmid = {39056112},
issn = {2042-650X},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Mice ; Rats ; *Depression/metabolism ; *Rats, Sprague-Dawley ; *Mice, Inbred C57BL ; *Inflammation/metabolism ; *Orexins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Orexin Receptors/metabolism/genetics ; Hippocampus/metabolism/drug effects ; 3T3-L1 Cells ; Microglia/metabolism/drug effects ; Phenotype ; Benzoxazoles ; Naphthyridines ; Urea/analogs &amp; derivatives ; },
abstract = {Background: A high-fat diet (HFD) is generally associated with an increased risk of mental disorders that constitute a sizeable worldwide health. A HFD results in the gut microbiota-brain axis being altered and linked to mental disorders. Hypocretin-1, which can promote appetite, has been previously confirmed to be associated with depression. However, no exact relationship has been found for hypocretin between depression and HFDs. Methods: Adult male SD rats were randomly assigned to either a HFD or a normal diet for eight weeks, followed by behavioral tests and plasma biochemical analyses. Then, we investigated the protein and mRNA levels of inflammation-related factors in the hippocampus. We also observed morphological changes in brain microglia and lipid accumulation. Additionally, metagenomic and metabolomic analyses of gut microbiomes were performed. 3T3-L1 cells were utilized in vitro to investigate the impact of hypocretin receptor 1 antagonists (SB334867) on lipid accumulation. To consider the connection between the brain and adipose tissue, we used a conditioned medium (CM) treated with 3T3-L1 cells to observe the activation and phagocytosis of BV2 cells. Following a 12-week period of feeding a HFD to C57BL/6 mice, a three-week intervention period was initiated during which the administration of SB334867 was observed. This was followed by a series of assessments, including monitoring of body weight changes and emotional problems, as well as attention to plasma biochemical levels and microglial cell phenotypes in the brain. Results: The HFD rats displayed anxiety and depressive-like behaviors. HFD rats exhibited increased plasma HDL, LDL, and TC levels. A HFD also causes an increase in hypocretin-1 and hypocretin-2 in the hypothalamus. Metagenomics and metabolomics revealed that the HFD caused an increase in the relative abundance of associated inflammatory bacteria and decreased the abundance of anti-inflammatory and bile acid metabolites. Compared with the CTR group, hippocampal microglia in the HFD group were significantly activated and accompanied by lipid deposition. At the same time, protein and mRNA expression levels of inflammation-related factors were increased. We found that SB334867 could significantly reduce lipid accumulation in 3T3-L1 cells after differentiation. The expression of inflammatory factors decreased in the SB334867 group. The administration of SB334867 was found to reverse the adverse effects of the HFD on body weight, depressive-like behaviour and anxiety-like mood. Furthermore, this treatment was associated with improvements in plasma biochemical levels and a reduction in the number of microglia in the brain. Conclusions: In summary, our results demonstrated that a HFD induced anxiety and depressive-like behaviors, which may be linked to the increased hypocretin-1 level and lipid accumulation. Supplementation with SB334867 improved the above. These observations highlight the possibility of hypocretin-1 inducing the risk of HFD-associated emotional dysfunctions.},
}
@article {pmid38996003,
year = {2024},
author = {Byndloss, M and Devkota, S and Duca, F and Hendrik Niess, J and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L},
title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.},
journal = {Diabetes care},
volume = {47},
number = {9},
pages = {1491-1508},
doi = {10.2337/dci24-0052},
pmid = {38996003},
issn = {1935-5548},
support = {//Novo Nordisk/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology ; Diabetes Mellitus/microbiology ; },
abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.},
}
@article {pmid38990271,
year = {2024},
author = {Ulger, Y and Delik, A and Akkız, H},
title = {Gut Microbiome and colorectal cancer: discovery of bacterial changes with metagenomics application in Turkısh population.},
journal = {Genes &amp; genomics},
volume = {46},
number = {9},
pages = {1059-1070},
pmid = {38990271},
issn = {2092-9293},
support = {148-TGD-2022//Turkish Gastroenterology Association/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Female ; Male ; *Metagenomics/methods ; Aged ; Turkey ; Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the 3rd most common cancer in the world and colonic carcinogenesis is a multifactorial disease that involves environmental and genetic factors. Gut microbiota plays a critical role in the regulation of intestinal homeostasis. Increasing evidence shows that the gut microbiome plays a role in CRC development and may be a biomarker for early diagnosis.<br><br>OBJECTIVE: This study aimed to determine the clinical prognostic significance of gut microbiota in CRC patients in the Turkish population by metagenomic analysis and to determine the microbial composition in tumor tissue biopsy samples.<br><br>METHODS: Tissue biopsies were taken from the participants with sterile forceps during colonoscopy and stored at -80&#xa0;&#xb0;C. Then, DNA isolation was performed from the tissue samples and the V3-V4 region of the 16&#xa0;S rRNA gene was sequenced on the Illumina MiSeq platform. Quality control of the obtained sequence data was performed. Operational taxonomic units (OTUs) were classified according to the Greengenes database. Alpha diversity (Shannon index) and beta diversity (Bray-Curtis distance) analyses were performed. The most common bacterial species in CRC patients and healthy controls were determined and whether there were statistically significant differences between the groups was tested.<br><br>RESULTS: A total of 40 individuals, 13 CRC patients and 20 healthy control individuals were included in our metagenomic study. The mean age of the patients was 64.83 and BMI was 25.85. In CRC patients, the level of Bacteroidetes at the phylum taxonomy was significantly increased (p&#x2009;=&#x2009;0.04), the level of Clostridia at the class taxonomy was increased (p&#x2009;=&#x2009;0.23), and the level of Enterococcus at the genus taxonomy was significantly increased (p&#x2009;=&#x2009;0.01). When CRC patients were compared with the control group, significant increases were detected in the species of Gemmiger formicilis (p&#x2009;=&#x2009;0.15), Prevotella copri (p&#x2009;=&#x2009;0.02) and Ruminococcus bromii (p&#x2009;=&#x2009;0.001) at the species taxonomy.<br><br>CONCLUSIONS: Metagenomic analysis of intestinal microbiota composition in CRC patients provides important data for determining the treatment options for these patients. The results of this study suggest that it may be beneficial in terms of early diagnosis, poor prognosis and survival rates in CRC patients. In addition, this metagenomic study is the first study on the colon microbiome associated with CRC mucosa in the Turkish population.},
}
@article {pmid39185088,
year = {2024},
author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L},
title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1369192},
doi = {10.3389/fcimb.2024.1369192},
pmid = {39185088},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; },
abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.<br><br>METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.<br><br>RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-&#x3b1; levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.<br><br>CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.},
}
@article {pmid39185086,
year = {2024},
author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W},
title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1410681},
doi = {10.3389/fcimb.2024.1410681},
pmid = {39185086},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; },
abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.<br><br>METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.<br><br>RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).<br><br>CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.},
}
@article {pmid39182301,
year = {2024},
author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C},
title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135567},
doi = {10.1016/j.jhazmat.2024.135567},
pmid = {39182301},
issn = {1873-3336},
abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.},
}
@article {pmid39182227,
year = {2024},
author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS},
title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2389319},
doi = {10.1080/19490976.2024.2389319},
pmid = {39182227},
issn = {1949-0984},
mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; },
abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.},
}
@article {pmid39182035,
year = {2024},
author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L},
title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {313},
pmid = {39182035},
issn = {1471-2180},
mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; },
abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.<br><br>RESULTS: At 31.5&#xa0;&#x3bc;M Cu, 112.4&#xa0;&#x3bc;M Ni and 122.3&#xa0;&#x3bc;M Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.<br><br>CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.},
}
@article {pmid39180208,
year = {2024},
author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y},
title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.},
journal = {Critical reviews in eukaryotic gene expression},
volume = {34},
number = {8},
pages = {59-73},
pmid = {39180208},
issn = {1045-4403},
mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.},
}
@article {pmid39127363,
year = {2024},
author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T},
title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.},
journal = {Bioresource technology},
volume = {409},
number = {},
pages = {131244},
doi = {10.1016/j.biortech.2024.131244},
pmid = {39127363},
issn = {1873-2976},
mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; },
abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.},
}
@article {pmid39122016,
year = {2024},
author = {Fiorucci, S and Marchianò, S and Urbani, G and Di Giorgio, C and Distrutti, E and Zampella, A and Biagioli, M},
title = {Immunology of bile acids regulated receptors.},
journal = {Progress in lipid research},
volume = {95},
number = {},
pages = {101291},
doi = {10.1016/j.plipres.2024.101291},
pmid = {39122016},
issn = {1873-2194},
mesh = {Humans ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Gastrointestinal Microbiome/immunology ; },
abstract = {Bile acids are steroids formed at the interface of host metabolism and intestinal microbiota. While primary bile acids are generated in the liver from cholesterol metabolism, secondary bile acids represent the products of microbial enzymes. Close to 100 different enzymatic modifications of bile acids structures occur in the human intestine and clinically guided metagenomic and metabolomic analyses have led to the identification of an extraordinary number of novel metabolites. These chemical mediators make an essential contribution to the composition and function of the postbiota, participating to the bidirectional communications of the intestinal microbiota with the host and contributing to the architecture of intestinal-liver and -brain and -endocrine axes. Bile acids exert their function by binding to a group of cell membrane and nuclear receptors collectively known as bile acid-regulated receptors (BARRs), expressed in monocytes, tissue-resident macrophages, CD4+ T effector cells, including Th17, T regulatory cells, dendritic cells and type 3 of intestinal lymphoid cells and NKT cells, highlighting their role in immune regulation. In this review we report on how bile acids and their metabolitesmodulate the immune system in inflammations and cancers and could be exploiting for developing novel therapeutic approaches in these disorders.},
}
@article {pmid39098060,
year = {2024},
author = {Cojkic, A and Niazi, A and Morrell, JM},
title = {Metagenomic identification of bull semen microbiota in different seasons.},
journal = {Animal reproduction science},
volume = {268},
number = {},
pages = {107569},
doi = {10.1016/j.anireprosci.2024.107569},
pmid = {39098060},
issn = {1873-2232},
mesh = {Male ; Animals ; *Seasons ; Cattle ; *Semen/microbiology ; *Microbiota ; *Semen Analysis/veterinary ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Spermatozoa/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {A seasonal effect on sperm quality parameters was observed previously. Although identification of the bull semen microbiota by 16S rRNA sequencing was performed previously, it has not been carried out in commercial semen samples from different seasons, and its connection with sperm quality parameters has not been evaluated yet. The objectives in this study were; (i) to evaluate diversity of bull semen microbiota and sperm quality parameters in different seasons, and (ii) to find if specific bacteria were associated with seasonal differences in specific sperm quality parameters. Bull semen microbiota was identified in 54 commercial bull semen samples from 3 seasons (winter, spring, summer). Sperm quality was analysed by Computer Assisted Sperm Analyses (CASA) and Flow Cytometry (FC). From 28 phyla in all samples, six phyla were identified in samples from all seasons, with observed seasonal differences in their distribution. At genus level, 388 genera were identified, of which 22 genera had a relative abundance over 1 % and showed seasonal differences in bacterial diversity, and 9 bacteria genera were present in all seasons. Differences between spring and summer (P < 0.05) were observed for live hydrogen peroxide positive sperm cells. A trend towards significance (0.10 > P > 0.05) was observed for some CASA kinematics (VCL and LIN) and FC parameters (High respiratory activity, and live hydrogen peroxide positive sperm cells) between seasons. Nevertheless, associations between sperm quality parameters and specific bacteria were observed in spring.},
}
@article {pmid39024692,
year = {2024},
author = {Chen, L and Bao, Y and Wang, D and Tian, Y and Zeng, T and Gu, T and Xu, W and Lu, L},
title = {Integrated omics analysis reveals the differentiation of intestinal microbiota and metabolites between Pekin ducks and Shaoxing ducks.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103976},
pmid = {39024692},
issn = {1525-3171},
mesh = {Animals ; *Ducks ; *Gastrointestinal Microbiome ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; },
abstract = {Pekin ducks and Shaoxing ducks are 2 Chinese local duck breeds, both domesticated from mallard, but after domestication and long-term artificial selection, the body weight of Pekin ducks is significantly higher than that of Shaoxing ducks. It is no debate that genetic factors are the main factors responsible for this difference, but whether intestinal microbiota contribute to this difference is yet unknown. Thus, we performed comparative intestinal metagenomics and metabolomics analysis between Pekin ducks and Shaoxing ducks. We found obvious differentiation of intestinal metagenome and metabolome between the 2 breeds. Four cecal microbial genera, including Fusobacterium, Methanobrevibacter, Butyricicoccus, and Anaerotignum showed higher abundance in Pekin ducks. Among them, Methanobrevibacter and Butyricicoccus may positively correlate with fat deposition and body weight. A total of 310 metabolites showed difference between the 2 breeds. Functions of these differential metabolites were mainly enriched in amino acid metabolism, including energy metabolism-related histidine metabolism. Integrated omics analysis showed that microbial changes were closely related to altered metabolites. Especially, Butyricicoccus showing higher abundance in Pekin ducks was significantly negatively correlated with D-glucosamine-6-phosphate, which has been reported to prevent body weight gains. These findings may contribute to further understand the difference in body weight between Pekin ducks and Shaoxing ducks.},
}
@article {pmid38945001,
year = {2024},
author = {Schäfer, L and Grundmann, SM and Rühl, M and Zorn, H and Seel, W and Simon, MC and Schuchardt, S and Most, E and Ringseis, R and Eder, K},
title = {Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103975},
pmid = {38945001},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Pleurotus ; *Animal Feed/analysis ; Male ; *Transcriptome ; *Liver/metabolism ; *Diet/veterinary ; *Metabolome ; *Mycelium ; *Dietary Supplements/analysis ; Random Allocation ; },
abstract = {Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 males, 1-day-old Cobb 500 broilers were randomly assigned to 3 different groups and fed 3 different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a 3-phase feeding system for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of 2 low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.},
}
@article {pmid38755047,
year = {2024},
author = {Wang, Y and Yao, J and Zhu, Y and Yin, Z and Zhao, X},
title = {Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {25},
number = {3},
pages = {239-249},
doi = {10.1016/j.ajg.2023.12.009},
pmid = {38755047},
issn = {2090-2387},
mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Dyspepsia/drug therapy/metabolism/microbiology ; *Disease Models, Animal ; Male ; Duodenum/metabolism/microbiology ; Intestinal Mucosa/metabolism/drug effects ; Colon/metabolism ; Drug Therapy, Combination ; },
abstract = {BACKGROUND AND STUDY AIMS: The integration of traditional Chinese medicine and Western medicine holds promise for the treatment of gastrointestinal disorders, which are influenced by intestinal microbiota and metabolites. This study reports a possible mechanism for the combination of Simo Decoction and Golden Bifid in functional dyspepsia (FD) by regulating intestinal microbiota and short-chain fatty acids (SCFAs).<br><br>PATIENTS AND METHODS: A mouse model of food stagnation was constructed and treated with Simo Decoction combined with different concentrations of Golden Bifid. Meta-genomics sequencing was conducted to analyze the cecum contents of the mice. Following analyses of the composition and abundance of intestinal microbiota, gas chromatography-mass spectrometry was performed to measure SCFAs in the colonic content of mice. Finally, ELISA was utilized to determine the levels of pro-inflammatory factors in the duodenal mucosa of mice and the infiltration of eosinophils in the duodenum was observed by immunohistochemical staining.<br><br>RESULTS: Combination of Simo Decoction and Golden Bifid more significantly alleviated dyspepsia in mice with food stagnation compared with Simo Decoction alone. The optimal ratio of combined treatment was 0.0075&#xa0;mL/g (body weight) Simo Decoction and 0.0032&#xa0;mg/g (body weight) Golden Bifid. The combined treatment increased the abundance of Bifidobacterium and Bacteroides in the intestine. The levels of SCFAs in the colonic contents of mice were increased after the combined treatment, contributing to diminished pro-inflammatory factors in the duodenal mucosa and reduced eosinophil infiltration.<br><br>CONCLUSION: Combination of Simo Decoction and Golden Bifid increases the abundance of Bacteroides and Bifidobacterium and promotes the production of SCFAs, which is instrumental for alleviation of FD.},
}
@article {pmid39180123,
year = {2024},
author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE},
title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {195},
pmid = {39180123},
issn = {1743-422X},
support = {1R01A|129822-01/NH/NIH HHS/United States ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation &amp; purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; },
abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.},
}
@article {pmid39180058,
year = {2024},
author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Gut microbiome structure and function in asymptomatic diverticulosis.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {105},
pmid = {39180058},
issn = {1756-994X},
support = {R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.<br><br>METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.<br><br>RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value&#x2009;=&#x2009;0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values&#x2009;=&#x2009;0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction&#x2009;=&#x2009;0.09).<br><br>CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.},
}
@article {pmid39178288,
year = {2024},
author = {Buscaglia, M and Iriarte, JL and Schulz, F and Díez, B},
title = {Adaptation strategies of giant viruses to low-temperature marine ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae162},
pmid = {39178288},
issn = {1751-7370},
abstract = {Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral (GOEV) database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.},
}
@article {pmid39103543,
year = {2024},
author = {Li, HZ and Peng, J and Yang, K and Zhang, Y and Chen, QL and Zhu, YG and Cui, L},
title = {Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management.},
journal = {Nature food},
volume = {5},
number = {8},
pages = {673-683},
pmid = {39103543},
issn = {2662-1355},
support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22241603//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; *Bacteria/metabolism/genetics ; *Phosphates/metabolism ; *Soil/chemistry ; *Fertilizers/analysis ; Single-Cell Analysis ; Microbiota/physiology ; Solubility ; },
abstract = {Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.},
}
@article {pmid39094546,
year = {2024},
author = {Li, Q and Wang, J and Lv, J and Liu, D and Xiao, S and Mo, J and Lu, Z and Qiu, R and Li, C and Tang, L and He, S and Tang, Z and Cheng, Q and Zhan, T},
title = {Total flavonoids of litchi Seed alleviates schistosomiasis liver fibrosis in mice by suppressing hepatic stellate cells activation and modulating the gut microbiomes.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {178},
number = {},
pages = {117240},
doi = {10.1016/j.biopha.2024.117240},
pmid = {39094546},
issn = {1950-6007},
mesh = {Animals ; *Hepatic Stellate Cells/drug effects/metabolism/pathology ; *Liver Cirrhosis/drug therapy/parasitology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Litchi/chemistry ; *Seeds/chemistry ; Schistosomiasis japonica/drug therapy/complications ; Cytokines/metabolism ; Schistosoma japonicum/drug effects/pathogenicity ; Male ; Liver/drug effects/pathology/parasitology ; },
abstract = {Infection with Schistosoma japonicum (S. japonicum) is an important zoonotic parasitic disease that causes liver fibrosis in both human and domestic animals. The activation of hepatic stellate cells (HSCs) is a crucial phase in the development of liver fibrosis, and inhibiting their activation can alleviate this progression. Total flavonoids of litchi seed (TFL) is a naturally extracted drug, and modern pharmacological studies have shown its anti-fibrotic and liver-protective effects. However, the role of TFL in schistosomiasis liver fibrosis is still unclear. This study investigated the therapeutic effects of TFL on liver fibrosis in S. japonicum infected mice and explored its potential mechanisms. Animal study results showed that TFL significantly reduced the levels of Interleukin-1β (IL-1β), Tumor Necrosis Factor-α (TNF-α), Interleukin-4 (IL-4), and Interleukin-6 (IL-6) in the serum of S. japonicum infected mice. TFL reduced the spleen index of mice and markedly improved the pathological changes in liver tissues induced by S. japonicum infection, decreasing the expression of alpha-smooth muscle actin (α-SMA), Collagen I and Collagen III protein in liver tissues. In vitro studies indicated that TFL also inhibited the activation of HCSs induced by Transforming Growth Factor-β1 (TGF-β1) and reduced the levels of α-SMA. Gut microbes metagenomics study revealed that the composition, abundance, and functions of the mice gut microbiomes changed significantly after S. japonicum infection, and TLF treatment reversed these changes. Therefore, our study indicated that TFL alleviated granulomatous lesions and improved S. japonicum induced liver fibrosis in mice by inhibiting the activation of HSCs and by improving the gut microbiomes.},
}
@article {pmid38981480,
year = {2024},
author = {Piperni, E and Nguyen, LH and Manghi, P and Kim, H and Pasolli, E and Andreu-Sánchez, S and Arrè, A and Bermingham, KM and Blanco-Míguez, A and Manara, S and Valles-Colomer, M and Bakker, E and Busonero, F and Davies, R and Fiorillo, E and Giordano, F and Hadjigeorgiou, G and Leeming, ER and Lobina, M and Masala, M and Maschio, A and McIver, LJ and Pala, M and Pitzalis, M and Wolf, J and Fu, J and Zhernakova, A and Cacciò, SM and Cucca, F and Berry, SE and Ercolini, D and Chan, AT and Huttenhower, C and Spector, TD and Segata, N and Asnicar, F},
title = {Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries.},
journal = {Cell},
volume = {187},
number = {17},
pages = {4554-4570.e18},
doi = {10.1016/j.cell.2024.06.018},
pmid = {38981480},
issn = {1097-4172},
mesh = {Humans ; *Blastocystis/metabolism ; *Gastrointestinal Microbiome ; *Diet ; Male ; *Obesity ; Female ; Blastocystis Infections ; Adult ; Middle Aged ; Intestines/parasitology/microbiology ; Cardiovascular Diseases/prevention &amp; control ; Metagenome ; },
abstract = {Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.},
}
@article {pmid38945213,
year = {2024},
author = {Si, HR and Wu, K and Su, J and Dong, TY and Zhu, Y and Li, B and Chen, Y and Li, Y and Shi, ZL and Zhou, P},
title = {Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats.},
journal = {Virologica Sinica},
volume = {39},
number = {4},
pages = {565-573},
doi = {10.1016/j.virs.2024.06.008},
pmid = {38945213},
issn = {1995-820X},
mesh = {*Chiroptera/virology ; Animals ; *Virome ; China ; *Coinfection/virology/veterinary/microbiology ; *Metagenomics ; *Severe acute respiratory syndrome-related coronavirus/genetics/isolation &amp; purification/classification ; Phylogeny ; Genome, Viral/genetics ; Disease Reservoirs/virology ; },
abstract = {Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.},
}
@article {pmid38909766,
year = {2024},
author = {Heil, BA and van Heule, M and Thompson, SK and Kearns, TA and Beckers, KF and Oberhaus, EL and King, G and Daels, P and Dini, P and Sones, JL},
title = {Metagenomic characterization of the equine endometrial microbiome during anestrus.},
journal = {Journal of equine veterinary science},
volume = {140},
number = {},
pages = {105134},
doi = {10.1016/j.jevs.2024.105134},
pmid = {38909766},
issn = {0737-0806},
mesh = {Animals ; Horses/microbiology ; Female ; *Endometrium/microbiology ; *Microbiota/genetics ; *Anestrus ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Estrus/physiology ; RNA, Bacterial/genetics/analysis ; },
abstract = {The equine uterus is highly interrogated during estrus prior to breeding and establishing pregnancy. Many studies in mares have been performed during estrus under the influence of high estrogen concentrations, including the equine estrual microbiome. To date, it is unknown how the uterine microbiome of the mare is influenced by cyclicity; while, the equine vaginal microbiome is stable throughout the estrous cycle. We hypothesized that differences would exist between the equine endometrial microbiome of mares in estrus and anestrus. The aim of this study was two-fold: to characterize the resident endometrial microbiome of healthy mares during anestrus and to compare this with estrus. Double-guarded endometrial swabs were taken from healthy mares during estrus (n = 16) and in the following non-breeding season during anestrus (n = 8). Microbial population was identified using 16S rRNA sequencing. Our results suggest that the equine uterine microbiome in estrus has a low diversity and low richness, while during anestrus, a higher diversity and higher richness were seen compared to estrus. Despite this difference, both the estrus and anestrus endometrial microbiome were dominated by Proteobacteria, Firmicutes, and Bacteroidota. The composition of the microbial community between anestrus and estrus was significantly different. This may be explained by the difference in the composition of the endometrial immune milieu based on the stage of the cycle. Further research investigating the function of the equine endometrial microbiome and dynamics changes within the uterine environment is required.},
}
@article {pmid38679334,
year = {2024},
author = {Fang, Y and Wang, J and Sun, J and Su, Z and Chen, S and Xiao, J and Ni, J and Hu, Z and He, Y and Shen, S and Deng, F},
title = {RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qīnghăi Province, China.},
journal = {Virologica Sinica},
volume = {39},
number = {4},
pages = {537-545},
doi = {10.1016/j.virs.2024.04.006},
pmid = {38679334},
issn = {1995-820X},
mesh = {Animals ; *Dermacentor/virology ; China ; *Phylogeny ; *Virome/genetics ; *Genome, Viral/genetics ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; RNA Viruses/genetics/classification/isolation &amp; purification ; Bunyaviridae/genetics/classification/isolation &amp; purification ; },
abstract = {Ticks are a major parasite on the Qīnghăi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species in this area remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qīnghăi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xīnjiāng tick-associated virus 1 (XJTAV1), and three novel viruses: Qīnghăi Lake virus 1, Qīnghăi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qīnghăi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses in the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. nuttalli ticks. A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses from sequencing data of other tick pools by using the putative M segment sequence of QHLV3. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.},
}
@article {pmid39177227,
year = {2024},
author = {Deng, Y and Nong, Z and Wei, M and Xu, Y and Luo, Y and Li, X and Zhao, R and Yang, Z and Pan, L},
title = {Characteristics and function of the gut microbiota in patients with IgA nephropathy via metagenomic sequencing technology.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2393754},
doi = {10.1080/0886022X.2024.2393754},
pmid = {39177227},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Middle Aged ; Moraxella/isolation &amp; purification/genetics ; Escherichia coli/isolation &amp; purification/genetics ; Acinetobacter/isolation &amp; purification/genetics ; Metagenome ; Young Adult ; },
abstract = {OBJECTIVE: The aim of this study was to investigate the characteristics and related functional pathways of the gut microbiota in patients with IgA nephropathy (IgAN) through metagenomic sequencing technology.<br><br>METHODS: We enrolled individuals with primary IgAN, including patients with normal and abnormal renal function. Additionally, we recruited healthy volunteers as the healthy control group. Stool samples were collected, and species and functional annotation were performed through fecal metagenome sequencing. We employed linear discriminant analysis effect size (LEfSe) analysis to identify significantly different bacterial microbiota and functional pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to annotate microbiota functions, and redundancy analysis (RDA) was performed to analyze the factors affecting the composition and distribution of the gut microbiota.<br><br>RESULTS: LEfSe analysis revealed differences in the gut microbiota between IgAN patients and healthy controls. The characteristic microorganisms in the IgAN group were classified as Escherichia coli, with a significantly greater abundance than that in the healthy control group (p&#x2009;<&#x2009;0.05). The characteristic microorganisms in the IgAN group with abnormal renal function were identified as Enterococcaceae, Moraxella, Moraxella, and Acinetobacter. KEGG functional analysis demonstrated that the functional pathways of the microbiota that differed between IgAN patients and healthy controls were related primarily to bile acid metabolism.<br><br>CONCLUSIONS: The status of the gut microbiota is closely associated not only with the onset of IgAN but also with the renal function of IgAN patients. The characteristic gut microbiota may serve as a promising diagnostic biomarker and therapeutic target for IgAN.},
}
@article {pmid39175056,
year = {2024},
author = {Sbardellati, DL and Vannette, RL},
title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {155},
pmid = {39175056},
issn = {2049-2618},
support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; },
mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; },
abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.},
}
@article {pmid39174663,
year = {2024},
author = {Jafari, M and Moghimi, H and Tirandaz, H and Ebrahim-Habibi, MB},
title = {Corrosion behavior of predominant Halodesulfovibrio in a marine SRB consortium and its mitigation using ZnO nanoparticles.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19545},
pmid = {39174663},
issn = {2045-2322},
mesh = {Corrosion ; *Zinc Oxide/chemistry/pharmacology ; *Biofilms/drug effects ; *Bioreactors/microbiology ; Steel/chemistry ; Nanoparticles/chemistry ; Microbial Consortia/drug effects ; },
abstract = {Formation of Sulfate Reducing Bacteria (SRB) biofilm accelerates microbiologically influenced corrosion (MIC). The aim of this study was to investigate both the corrosivity of a marine SRB consortium on carbon steel coupons and its mitigation in the presence of ZnO. Metagenomics analysis revealed that Halodesulfovibrio (78.9%) was predominant and could be related to MIC. The analysis also showed a remarkable shift from a highly corrosive SRB consortium in the control bioreactors to a far less corrosive consortium when ZnO was added to the bioreactors. Further results indicated that the corrosion rate of the SRB consortium was 8.17 mpy on the carbon steel coupons. In the ZnO-treated bioreactors, the count of SRB and MIC in the carbon steel coupons simultaneously reduced. Moreover, Confocal Laser Scanning Microscopy and profilometry analysis determined that ZnO could significantly decrease the amount of biofilm and the corrosion rate. Electrochemical experiments revealed higher corrosion current density (icorr) and lower charge transfer resistance (Rct) in the control bioreactors relative to the ZnO-treated bioreactors. We introduce Halodesulfovibrio as a potentially important corrosive genus in a marine SRB consortium. Additionally, ZnO could be considered a proper candidate to control the corrosion induced by Halodesulfovibrio.},
}
@article {pmid39173234,
year = {2024},
author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT},
title = {Soil keystone viruses are regulators of ecosystem multifunctionality.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108964},
doi = {10.1016/j.envint.2024.108964},
pmid = {39173234},
issn = {1873-6750},
abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.},
}
@article {pmid39167702,
year = {2024},
author = {Prins, FM and Hidding, IJ and Klaassen, MAY and Collij, V and Schultheiss, JPD and Uniken Venema, WTC and Bangma, A and Aardema, JB and Jansen, BH and Mares, WGN and Witteman, BJM and Festen, EAM and Dijkstra, G and Visschedijk, MC and Fidder, HH and Vich Vila, A and Oldenburg, B and Gacesa, R and Weersma, RK},
title = {Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2391505},
doi = {10.1080/19490976.2024.2391505},
pmid = {39167702},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Metabolome/drug effects ; *Ustekinumab/therapeutic use ; Prospective Studies ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Feces/microbiology ; Female ; Male ; Adult ; Biological Therapy/methods ; Treatment Outcome ; Middle Aged ; Bacteria/genetics/classification/metabolism/drug effects/isolation &amp; purification ; Biomarkers/analysis/metabolism ; },
abstract = {Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.},
}
@article {pmid39089548,
year = {2024},
author = {Zeng, X and Tang, S and Dong, X and Dong, M and Shao, R and Liu, R and Li, T and Zhang, X and Wong, YH and Xie, Q},
title = {Analysis of metagenome and metabolome disclosed the mechanisms of Dendrobium officinale polysaccharide on DSS-induced ulcerative colitis-affected mice.},
journal = {International journal of biological macromolecules},
volume = {277},
number = {Pt 2},
pages = {134229},
doi = {10.1016/j.ijbiomac.2024.134229},
pmid = {39089548},
issn = {1879-0003},
mesh = {Animals ; *Dendrobium/chemistry ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Dextran Sulfate/adverse effects ; Mice ; *Metabolome/drug effects ; Male ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Antioxidants/pharmacology ; Disease Models, Animal ; },
abstract = {Currently, there is no known cause for ulcerative colitis (UC), an inflammatory bowel disease that is difficult to treat. This assay aimed to investigate the protective effects and mechanisms of Dendrobium officinale polysaccharide (DOP) in mice with acute UC induced by dextran sulphate sodium (DSS). We found that DOP could improve weight loss, decrease the disease activity index (DAI), and regulate the release of interleukin 2 (IL-2), IL-4, IL-6, and IL-10 in DSS-induced acute UC mice. Additionally, DOP preserved the integrity of the intestinal barrier in UC mice by increasing goblet cell density and maintaining tight junctions. DOP significantly enhanced total antioxidant capacity (T-AOC), and reduced glutathione (GSH), nitric oxide (NO), and malondialdehyde (MDA) levels in the bloodstream. In terms of serum biochemistry, DOP markedly elevated levels of bilirubin (BIL), alkaline phosphatase (ALP), total bile acid (TBA), creatinine (Crea), and creative kinase isoenzyme (CKMB). Furthermore, DOP increased the relative abundance of Lactobacillales. DOP also improved intestinal health and stimulated the synthesis of potent anti-inflammatory and antiviral substances by regulating the metabolism of purines, prostaglandins, and leukotrienes. Therefore, DOP can be considered a functional dietary supplement for the treatment of UC, as it improves the condition of DSS-induced UC mice.},
}
@article {pmid39033825,
year = {2024},
author = {Dong, Z and Han, K and Xie, Q and Lin, C and Shen, X and Hao, Y and Li, J and Xu, H and He, L and Yu, T and Kuang, W},
title = {Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {363},
number = {},
pages = {507-519},
doi = {10.1016/j.jad.2024.07.106},
pmid = {39033825},
issn = {1573-2517},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Depressive Disorder, Major/drug therapy/genetics/microbiology ; Female ; Male ; Adult ; Middle Aged ; Drug Resistance, Microbial/genetics ; Case-Control Studies ; },
abstract = {INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway.<br><br>METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed.<br><br>RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD.<br><br>LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion.<br><br>CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.},
}
@article {pmid39164259,
year = {2024},
author = {Seong, HJ and Kim, JJ and Kim, T and Ahn, SJ and Rho, M and Lee, KJ and Sul, WJ},
title = {Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {902},
pmid = {39164259},
issn = {2052-4463},
mesh = {Republic of Korea ; *Metagenome ; *Aquaculture ; Animals ; Bacteria/genetics/classification ; Microbiota ; Ostreidae/microbiology ; Archaea/genetics ; Pectinidae/microbiology/genetics ; Penaeidae/microbiology/genetics ; },
abstract = {The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.},
}
@article {pmid39160620,
year = {2024},
author = {Yu, T and Luo, Y and Tan, X and Zhao, D and Bi, X and Li, C and Zheng, Y and Xiang, H and Hu, S},
title = {Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {22},
number = {2},
pages = {},
doi = {10.1093/gpbjnl/qzad006},
pmid = {39160620},
issn = {2210-3244},
support = {//Center for Ocean Mega-Science, Chinese Academy of Sciences/ ; 2021QZKK0100//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Biological Products/metabolism ; Cold Temperature ; Phylogeny ; Seawater/microbiology ; Metagenomics/methods ; Biodiversity ; },
abstract = {Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.},
}
@article {pmid39078126,
year = {2024},
author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P},
title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0069524},
doi = {10.1128/aem.00695-24},
pmid = {39078126},
issn = {1098-5336},
mesh = {*Composting ; Gene Transfer, Horizontal ; Manure/microbiology/virology ; Soil Microbiology ; Bacteria/genetics/drug effects ; Animals ; Metagenome ; Cattle ; Hot Temperature ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Microbiota ; Bacteriophages/genetics/physiology ; },
abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.<br><br>IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.},
}
@article {pmid38922379,
year = {2024},
author = {Mikó, E and Sipos, A and Tóth, E and Lehoczki, A and Fekete, M and Sebő, &#xc9; and Kardos, G and Bai, P},
title = {Guideline for designing microbiome studies in neoplastic diseases.},
journal = {GeroScience},
volume = {46},
number = {5},
pages = {4037-4057},
pmid = {38922379},
issn = {2509-2723},
support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; FK146852//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; TKP2021-EGA-19//NFKIH/ ; POST-COVID2021-33//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; NKM2022-30//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Research Design ; },
abstract = {Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.},
}
@article {pmid39094704,
year = {2024},
author = {Dang, S and Fan, W and Meng, F and Li, X and Hao, J and Wang, C},
title = {Decolorization and detoxification of direct blue 5B by a Marinobacter-dominated halo-thermoalkalophilic consortium.},
journal = {Chemosphere},
volume = {363},
number = {},
pages = {142957},
doi = {10.1016/j.chemosphere.2024.142957},
pmid = {39094704},
issn = {1879-1298},
mesh = {*Marinobacter/metabolism/genetics ; *Biodegradation, Environmental ; Azo Compounds/metabolism/chemistry ; Coloring Agents/metabolism/chemistry ; Microbial Consortia ; Salinity ; Sewage/microbiology ; Hydrogen-Ion Concentration ; Temperature ; Water Pollutants, Chemical/metabolism/analysis ; Oryza ; },
abstract = {Azo dye-containing sewage is commonly detected at high salinity, temperature and pH. In this study, a halo-thermoalkalophilic azo dye decolorization consortium was enriched and named "consortium HL". Consortium HL which was dominated by Marinobacter (84.30%), Desulfocurvibacter (1.89%), and Pseudomonas (1.85%), was able to completely decolorize Direct Blue 5B (DB5) during incubation with the material at 5% salinity, 50 °C, and pH 9 for 30 h. The decolorization mechanism was proposed based on combined metagenomic analysis, GC‒MS, and enzymatic activity detection. The action of the consortium HL showed great tolerance to variations in salinity, temperature and pH. A phytotoxicity study indicated that the metabolic intermediates showed no significant toxicity to the generation of Cucumis sativus and Oryza sativa seeds. This study, in which azo dye decolorization and degradation under high-salt, high-temperature and high-alkalinity conditions were investigated and deeply analyzed by metagenomic information, is the first report regarding the ability of Marinobacter to decolorize azo dyes at high temperatures.},
}
@article {pmid39082797,
year = {2024},
author = {Roager, L and Kempen, PJ and Bentzon-Tilia, M and Sonnenschein, EC and Gram, L},
title = {Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0058324},
doi = {10.1128/msystems.00583-24},
pmid = {39082797},
issn = {2379-5077},
support = {NNF20OC0064249,NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; },
mesh = {*Microbiota/physiology ; *Diatoms ; *Microalgae ; *RNA, Ribosomal, 16S/genetics ; *Haptophyta ; Chlorophyta/microbiology ; Seawater/microbiology ; },
abstract = {UNLABELLED: Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte Isochrysis galbana, the chlorophyte Tetraselmis suecica, and the diatom Conticribra weissflogii (previously Thalassiosira), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but I. galbana microbiomes diverged further from T. suecica and C. weissflogii microbiomes. I. galbana microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of I. galbana affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of I. galbana microbiomes diverging further from those of T. suecica and C. weissflogii microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of C. weissflogii, which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host.<br><br>IMPORTANCE: As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.},
}
@article {pmid39078158,
year = {2024},
author = {Jin, D-M and Morton, JT and Bonneau, R},
title = {Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0029524},
doi = {10.1128/msystems.00295-24},
pmid = {39078158},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Diabetes Mellitus, Type 2/microbiology ; Machine Learning ; Crohn Disease/microbiology ; Colorectal Neoplasms/microbiology ; Metagenomics/methods ; Colitis, Ulcerative/microbiology ; Parkinson Disease/microbiology ; Schizophrenia/microbiology ; Alzheimer Disease/microbiology ; },
abstract = {UNLABELLED: Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings, detected by our pipeline, provide valuable insights into these diseases.<br><br>IMPORTANCE: Assessing disease similarity is an essential initial step preceding a disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual diseases to understand their unique characteristics, which by design excludes comorbidities in individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilizes both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.},
}
@article {pmid39012154,
year = {2024},
author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS},
title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0062724},
doi = {10.1128/msystems.00627-24},
pmid = {39012154},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; },
abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.<br><br>IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.},
}
@article {pmid38990071,
year = {2024},
author = {Spirito, CM and Lucas, TN and Patz, S and Jeon, BS and Werner, JJ and Trondsen, LH and Guzman, JJ and Huson, DH and Angenent, LT},
title = {Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0041624},
doi = {10.1128/msystems.00416-24},
pmid = {38990071},
issn = {2379-5077},
support = {STAR Fellowship//U.S. Environmental Protection Agency (EPA)/ ; Alexander von Humboldt Professorship//Alexander von Humboldt-Stiftung (AvH)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; NNF21SA0072700//Novo Nordisk Fonden (NNF)/ ; W911NF-12-1-0555//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; Collaboration between the University of Maryland and the University of T&#xfc;bingen//Reinhard Frank Stiftung/ ; },
mesh = {*Bioreactors/microbiology ; *Microbiota ; Caprylates/metabolism ; Caproates/metabolism ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Liquid-Liquid Extraction/methods ; },
abstract = {Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as n-caproate (C6) and n-caprylate (C8), from organic substrates such as wastes. Even though the production of n-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for n-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed. n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2 and O2 between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the Clostridia class. Several Oscillibacter spp., including Oscillibacter valericigenes, were positively correlated with n-caprylate production rates, while Clostridium kluyveri was positively correlated with n-caproate production. Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of n-caprylate production rates. This study provides insight into microbiota that are associated with n-caprylate production in open-culture reactors and provides ideas for further work.IMPORTANCEMicrobial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including n-caproate (C6) and n-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for n-caproate or n-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from n-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.},
}
@article {pmid38980054,
year = {2024},
author = {Duller, S and Kumpitsch, C and Moissl-Eichinger, C and Wink, L and Koskinen Mora, K and Mahnert, A},
title = {In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0072624},
doi = {10.1128/msystems.00726-24},
pmid = {38980054},
issn = {2379-5077},
support = {//Medizinische Universit&#xe4;t Wien (MediUni Wien)/ ; },
mesh = {Humans ; *Microbiota/drug effects/genetics ; Hospitals ; Cross Infection/microbiology ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {UNLABELLED: Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.<br><br>IMPORTANCE: Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.},
}
@article {pmid38980053,
year = {2024},
author = {Sanguineti, D and Zampieri, G and Treu, L and Campanaro, S},
title = {Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0021324},
doi = {10.1128/msystems.00213-24},
pmid = {38980053},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Software ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.},
}
@article {pmid38980052,
year = {2024},
author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH},
title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0057324},
doi = {10.1128/msystems.00573-24},
pmid = {38980052},
issn = {2379-5077},
support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; },
abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.<br><br>IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.},
}
@article {pmid38975760,
year = {2024},
author = {Tang-Wing, C and Mohanty, I and Bryant, M and Makowski, K and Melendez, D and Dorrestein, PC and Knight, R and Caraballo-Rodríguez, AM and Allaband, C and Jenné, K},
title = {Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus).},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0010824},
doi = {10.1128/msystems.00108-24},
pmid = {38975760},
issn = {2379-5077},
support = {S10 OD026929/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; *Callithrix/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet/veterinary ; Male ; Female ; Feces/microbiology ; Bifidobacterium/isolation &amp; purification ; },
abstract = {UNLABELLED: Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change.<br><br>IMPORTANCE: Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.},
}
@article {pmid38918932,
year = {2024},
author = {Tian, B and Xu, LL and Jiang, LD and Lin, X and Shen, J and Shen, H and Su, KJ and Gong, R and Qiu, C and Luo, Z and Yao, JH and Wang, ZQ and Xiao, HM and Zhang, LS and Deng, HW},
title = {Identification of the serum metabolites associated with cow milk consumption in Chinese Peri-/Postmenopausal women.},
journal = {International journal of food sciences and nutrition},
volume = {75},
number = {6},
pages = {537-549},
doi = {10.1080/09637486.2024.2366223},
pmid = {38918932},
issn = {1465-3478},
mesh = {Humans ; Female ; *Milk ; Animals ; Middle Aged ; *Postmenopause/blood ; China ; *Gastrointestinal Microbiome ; Cattle ; Citrulline/blood ; Aged ; Diet ; Metabolome ; Bacteroides ; East Asian People ; },
abstract = {Cow milk consumption (CMC) and downstream alterations of serum metabolites are commonly considered important factors regulating human health status. Foods may lead to metabolic changes directly or indirectly through remodelling gut microbiota (GM). We sought to identify the metabolic alterations in Chinese Peri-/Postmenopausal women with habitual CMC and explore if the GM mediates the CMC-metabolite associations. 346 Chinese Peri-/Postmenopausal women participants were recruited in this study. Fixed effects regression and partial least squares discriminant analysis (PLS-DA) were applied to reveal alterations of serum metabolic features in different CMC groups. Spearman correlation coefficient was computed to detect metabolome-metagenome association. 36 CMC-associated metabolites including palmitic acid (FA(16:0)), 7alpha-hydroxy-4-cholesterin-3-one (7alphaC4), citrulline were identified by both fixed effects regression (FDR < 0.05) and PLS-DA (VIP score > 2). Some significant metabolite-GM associations were observed, including FA(16:0) with gut species Bacteroides ovatus, Bacteroides sp.D2. These findings would further prompt our understanding of the effect of cow milk on human health.},
}
@article {pmid38912690,
year = {2024},
author = {Byndloss, M and Devkota, S and Duca, F and Niess, JH and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L},
title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.},
journal = {Diabetes},
volume = {73},
number = {9},
pages = {1391-1410},
doi = {10.2337/dbi24-0028},
pmid = {38912690},
issn = {1939-327X},
support = {2020 (09150182010020)//ZONMW-VICI/ ; 875534//European Union&#xe2;&#x20ac;&#x2122;s Innovative Medicine Initiative/ ; 310030_219210//Swiss National Science Foundation (SNSF)/ ; CEX2021-001189-S/10.13039/501100011033//Severo Ochoa Center of Excellence/ ; //Novo Nordisk Foundation/ ; 2020 (2020.10.002)//DFN-DON/ ; 1DP1 DK130687/DK/NIDDK NIH HHS/United States ; PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities MICIU/AEI/ ; 1DP1 DK130687/DK/NIDDK NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/therapy ; Translational Research, Biomedical ; },
abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.},
}
@article {pmid39160043,
year = {2024},
author = {Merino, N and Pagán, E and Berdejo, D and Worby, CJ and Young, M and Manson, AL and Pagán, R and Earl, AM and García-Gonzalo, D},
title = {Dynamics of microbiome and resistome in a poultry burger processing line.},
journal = {Food research international (Ottawa, Ont.)},
volume = {193},
number = {},
pages = {114842},
doi = {10.1016/j.foodres.2024.114842},
pmid = {39160043},
issn = {1873-7145},
mesh = {Animals ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Food Handling/methods ; Poultry/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Meat/microbiology ; Poultry Products/microbiology ; },
abstract = {Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&amp;D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&amp;D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&amp;D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.},
}
@article {pmid39160615,
year = {2024},
author = {Hugerth, LW and Krog, MC and Vomstein, K and Du, J and Bashir, Z and Kaldhusdal, V and Fransson, E and Engstrand, L and Nielsen, HS and Schuppe-Koistinen, I},
title = {Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {153},
pmid = {39160615},
issn = {2049-2618},
support = {KAW 2020.0239//Science for Life Laboratory/ ; E-22614-01, E-22614-02//Rigshospitalet/ ; 2021-01683//Vetenskapsr&#xe5;det/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Menstruation ; *Bacteria/classification/genetics ; Adult ; *Dysbiosis/microbiology ; *Menstrual Cycle ; Young Adult ; Genes, Bacterial/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.<br><br>RESULTS: Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.<br><br>CONCLUSIONS: The VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.},
}
@article {pmid39157177,
year = {2024},
author = {Huang, SS and Qiu, JY and Li, SP and Ma, YQ and He, J and Han, LN and Jiao, LL and Xu, C and Mao, YM and Zhang, YM},
title = {Microbial signatures predictive of short-term prognosis in severe pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1397717},
pmid = {39157177},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Prognosis ; Retrospective Studies ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; Pneumonia/microbiology/mortality ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Lung/microbiology/pathology ; Metagenomics ; Machine Learning ; },
abstract = {OBJECTIVE: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis.<br><br>METHODS: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis.<br><br>RESULTS: The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial &#x3b1; and &#x3b2; diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera.<br><br>CONCLUSION: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.},
}
@article {pmid39154041,
year = {2024},
author = {Ma, T and Zhuang, Y and Lu, W and Tu, Y and Diao, Q and Fan, X and Zhang, N},
title = {Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {897},
pmid = {39154041},
issn = {2052-4463},
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology ; *Metagenome ; Gastrointestinal Microbiome ; },
abstract = {The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.},
}
@article {pmid38918632,
year = {2024},
author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD},
title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.},
journal = {Nature medicine},
volume = {30},
number = {8},
pages = {2265-2276},
pmid = {38918632},
issn = {1546-170X},
support = {R00DK119412//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01NR01999//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AG077489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30DK046200//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Phylogeny ; Cohort Studies ; Male ; Middle Aged ; Female ; China/epidemiology ; Dysbiosis/microbiology ; United States/epidemiology ; Israel/epidemiology ; Europe/epidemiology ; },
abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.},
}
@article {pmid39153763,
year = {2024},
author = {Cleminson, JS and Thomas, J and Stewart, CJ and Campbell, D and Gennery, A and Embleton, ND and Köglmeier, J and Wong, T and Spruce, M and Berrington, JE},
title = {Gut microbiota and intestinal rehabilitation: a prospective childhood cohort longitudinal study of short bowel syndrome (the MIRACLS study): study protocol.},
journal = {BMJ open gastroenterology},
volume = {11},
number = {1},
pages = {},
doi = {10.1136/bmjgast-2024-001450},
pmid = {39153763},
issn = {2054-4774},
mesh = {Humans ; *Short Bowel Syndrome/microbiology/epidemiology ; *Gastrointestinal Microbiome/physiology ; *Quality of Life/psychology ; Prospective Studies ; Child ; Child, Preschool ; Infant ; Longitudinal Studies ; Female ; Adolescent ; *Feces/microbiology ; Male ; *Parenteral Nutrition/methods/statistics &amp; numerical data ; Infant, Newborn ; RNA, Ribosomal, 16S ; Intestines/microbiology ; },
abstract = {INTRODUCTION: Short bowel syndrome (SBS) is the predominant cause of paediatric intestinal failure. Although life-saving, parenteral nutrition (PN) is linked to complications and may impact quality of life (QoL). Most children will experience intestinal rehabilitation (IR), but the mechanisms underpinning this remain to be understood. SBS is characterised by abnormal microbiome patterns, which might serve as predictive indicators for IR. We aim to characterise the microbiome profiles of children with SBS during IR, concurrently exploring how parental perspectives of QoL relate to IR.<br><br>METHODS AND ANALYSIS: This study will enrol a minimum of 20 paediatric patients with SBS (0-18 years). Clinical data and biological samples will be collected over a 2-year study period. We will apply 16S rRNA gene sequencing to analyse the microbiome from faecal and gut tissue samples, with additional shotgun metagenomic sequencing specifically on samples obtained around the time of IR. Gas chromatography with flame ionisation detection will profile faecal short-chain fatty acids. Plasma citrulline and urinary intestinal fatty acid binding proteins will be measured annually. We will explore microbiome-clinical covariate interactions. Furthermore, we plan to assess parental perspectives on QoL during PN and post-IR by inviting parents to complete the Paediatric Quality of Life questionnaire at recruitment and after the completion of IR.<br><br>ETHICS AND DISSEMINATION: Ethical approval was obtained from the East Midlands-Nottingham 2 Research Ethics Committee (22/EM/0233; 28 November 2022). Recruitment began in February 2023. Outcomes of the study will be published in peer-reviewed scientific journals and presented at scientific meetings. A lay summary of the results will be made available to participants and the public.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN90620576.},
}
@article {pmid39152482,
year = {2024},
author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y},
title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {152},
pmid = {39152482},
issn = {2049-2618},
support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; },
abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.<br><br>RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants &#x2206;cysJ and &#x2206;cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.<br><br>CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.},
}
@article {pmid38977080,
year = {2024},
author = {Lichtenegger, AS and Posadas-Cantera, S and Badr, MT and Häcker, G},
title = {Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing.},
journal = {Journal of microbiological methods},
volume = {224},
number = {},
pages = {106988},
doi = {10.1016/j.mimet.2024.106988},
pmid = {38977080},
issn = {1872-8359},
mesh = {Humans ; *Culture Media/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria, Anaerobic/genetics/isolation &amp; purification/classification/growth &amp; development ; *Gastrointestinal Microbiome ; *DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; Bacteria/genetics/classification/isolation &amp; purification/drug effects/growth &amp; development ; },
abstract = {The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.},
}
@article {pmid38750900,
year = {2024},
author = {Lewis, JD and Daniel, SG and Li, H and Hao, F and Patterson, AD and Hecht, AL and Brensinger, CM and Wu, GD and Bittinger, K and , and , },
title = {Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {18},
number = {3},
pages = {101357},
pmid = {38750900},
issn = {2352-345X},
mesh = {Humans ; *Crohn Disease/microbiology/surgery/pathology/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; *Metabolome ; Prospective Studies ; *Feces/microbiology ; *Dysbiosis/microbiology ; Middle Aged ; Bile Acids and Salts/metabolism ; Butyrates/metabolism ; Metagenomics/methods ; Cholestenones/metabolism ; Ileum/microbiology/surgery/metabolism/pathology ; Young Adult ; Bacteria/isolation &amp; purification/classification/metabolism/genetics ; },
abstract = {BACKGROUND &amp; AIMS: Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery.<br><br>METHODS: Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies. Stool samples were analyzed with shotgun metagenomics sequencing. Fecal butyrate was measured with [1]H nuclear magnetic resonance spectroscopy. Fecal bile acids and plasma 7&#x3b1;-hydroxy-4-cholesten-3-one (C4) was measured with mass spectrometry.<br><br>RESULTS: Intestinal resection was associated with reduced alpha diversity and altered beta diversity with increased Proteobacteria and reduced Bacteroidetes and Firmicutes. Surgery was associated with higher representation of genes in the KEGG pathway for ABC transporters and reduction in genes related to bacterial metabolism. Surgery was associated with reduced concentration of the But gene but this did not translate to reduced fecal butyrate concentration. Surgery was associated with decreased abundance of bai operon genes, with increased plasma C4 concentration, increased primary bile acids and reduced secondary bile acids, including isoLCA. Additionally, Egerthella lenta, Adlercreutzia equalofaciens, and Gordonibacter pamelaeae were lower in abundance among patients with prior surgery in both cohorts.<br><br>CONCLUSIONS: In 2 different populations, prior surgery in Crohn's disease is associated with altered fecal microbiome. Patients who had undergone ileal resection had reduction in the potentially beneficial bacteria E lenta and related actinobacteria and secondary bile acids, including isoLCA, suggesting that these could be biomarkers of patients at higher risk for disease progression.},
}
@article {pmid39152146,
year = {2024},
author = {Mizsei, E and Radovics, D and Rák, G and Budai, M and Bancsik, B and Szabolcs, M and Sos, T and Lengyel, S},
title = {Alpine viper in changing climate: thermal ecology and prospects of a cold-adapted reptile in the warming Mediterranean.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18988},
pmid = {39152146},
issn = {2045-2322},
support = {150510498//Mohamed bin Zayed Species Conservation Fund/ ; 15478-1//Rufford Foundation/ ; PD146621//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; K106133//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; K134391//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal,Hungary/ ; },
mesh = {Animals ; *Viperidae/physiology ; *Climate Change ; Male ; Female ; Ecosystem ; Body Temperature Regulation/physiology ; Greece ; Cold Temperature ; Adaptation, Physiological ; Mediterranean Region ; Acclimatization/physiology ; Phylogeny ; Body Temperature/physiology ; },
abstract = {In a rapidly changing thermal environment, reptiles are primarily dependent on in situ adaptation because of their limited ability to disperse and the restricted opportunity to shift their ranges. However, the rapid pace of climate change may surpass these adaptation capabilities or elevate energy expenditures. Therefore, understanding the variability in thermal traits at both individual and population scales is crucial, offering insights into reptiles' vulnerability to climate change. We studied the thermal ecology of the endangered Greek meadow viper (Vipera graeca), an endemic venomous snake of fragmented alpine-subalpine meadows above 1600 m of the Pindos mountain range in Greece and Albania, to assess its susceptibility to anticipated changes in the alpine thermal environment. We measured preferred body temperature in artificial thermal gradient, field body temperatures of 74 individuals in five populations encompassing the entire geographic range of the species, and collected data on the available of temperatures for thermoregulation. We found that the preferred body temperature (Tp) differed only between the northernmost and the southernmost populations and increased with female body size but did not depend on sex or the gravidity status of females. Tp increased with latitude but was unaffected by the phylogenetic position of the populations. We also found high accuracy of thermoregulation in V. graeca populations and variation in the thermal quality of habitats throughout the range. The overall effectiveness of thermoregulation was high, indicating that V. graeca successfully achieves its target temperatures and exploits the thermal landscape. Current climatic conditions limit the activity period by an estimated 1278 h per year, which is expected to increase considerably under future climate scenarios. Restricted time available for thermoregulation, foraging and reproduction will represent a serious threat to the fitness of individuals and the persistence of populations in addition to habitat loss due to mining, tourism or skiing and habitat degradation due to overgrazing in the shrinking mountaintop habitats of V. graeca.},
}
@article {pmid39151620,
year = {2024},
author = {Zheng, Y and Wu, Z and Wang, P and Wei, Y and Jia, K and Zhang, M and Shi, X and Zhang, L and Li, J},
title = {Long-chain fatty acids facilitate acidogenic fermentation of food waste: Attention to the microbial response and the change of core metabolic pathway under saturated and unsaturated fatty acids loading.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175565},
doi = {10.1016/j.scitotenv.2024.175565},
pmid = {39151620},
issn = {1879-1026},
abstract = {Long-chain fatty acids (LCFAs) are recognized as a significant inhibitory factor in anaerobic digestion of food waste (FW), yet they are inevitably present in FW due to lipid hydrolysis. Given their distinct synthesis mechanism from traditional anaerobic digestion, little is known about the effect of LCFAs on FW acidogenic fermentation. This study reveals that total volatile fatty acids (VFAs) production increased by 9.98 % and 4.03 % under stearic acid and oleic acid loading, respectively. Acetic acid production increased by 20.66 % under stearic acid loading compared to the control group (CK). However, the LCFA stress restricted the degradation of solid organic matter, particularly under oleic acid stress. Analysis of microbial community structure and quorum sensing (QS) indicates that LCFA stress enhanced the relative abundance of Lactobacillus and Klebsiella. In QS system, the relative abundance of luxS declined from 0.157 % to 0.116 % and 0.125 % under oleic acid and stearic acid stress, respectively. LCFA stress limited the Autoinducer-2 (AI-2) biosynthesis, suggesting that microorganisms cannot use QS to resist the LCFA stress. Metagenomic sequencing showed that LCFA stress promoted acetic acid production via the conversion of pyruvate and acetyl-CoA to acetate. Direct conversion of pyruvate to acetic acid increased by 47.23 % compared to the CK group, accounting for the enhanced acetic acid production under stearic acid loading. The abundance of β-oxidation pathway under stearic acid loading was lower than under oleic acid loading. Overall, the stimulating direct conversion of pyruvate plays a pivotal role in enhancing acetic acid biosynthesis under stearic acid loading, providing insights into the effect of LCFA on mechanism of FW acidogenic fermentation.},
}
@article {pmid39147529,
year = {2024},
author = {Xiang, L and Zhuo, S and Luo, W and Tian, C and Xu, S and Li, X and Zhu, Y and Feng, R and Chen, M},
title = {Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114852},
doi = {10.1016/j.foodres.2024.114852},
pmid = {39147529},
issn = {1873-7145},
mesh = {Humans ; *Crohn Disease/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/physiology ; *Polyphenols/metabolism ; Female ; Male ; Adult ; *Diet ; Hippurates/metabolism ; Middle Aged ; Young Adult ; Bacteria/classification/metabolism/genetics ; Feces/microbiology ; },
abstract = {Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.},
}
@article {pmid39053208,
year = {2024},
author = {Kong, Z and Wang, H and Wang, H and Man, S and Yan, Q},
title = {Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics.},
journal = {Water research},
volume = {262},
number = {},
pages = {122132},
doi = {10.1016/j.watres.2024.122132},
pmid = {39053208},
issn = {1879-2448},
mesh = {*Denitrification ; *Ferrosoferric Oxide/metabolism ; Geobacter/metabolism ; Nitrates/metabolism ; Microbial Consortia ; Bioreactors/microbiology ; },
abstract = {Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm[2], would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.},
}
@article {pmid39043054,
year = {2024},
author = {Perdomo, A and Calle, A},
title = {Assessment of microbial communities in a dairy farm from a food safety perspective.},
journal = {International journal of food microbiology},
volume = {423},
number = {},
pages = {110827},
doi = {10.1016/j.ijfoodmicro.2024.110827},
pmid = {39043054},
issn = {1879-3460},
mesh = {Animals ; *Food Safety ; *Dairying ; Cattle ; *Farms ; *Milk/microbiology ; Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Food Microbiology ; Feces/microbiology ; Seasons ; Animal Feed/microbiology ; Staphylococcus aureus/isolation &amp; purification/genetics ; },
abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.},
}
@article {pmid39032335,
year = {2024},
author = {Fan, Y and Zhou, Z and Liu, F and Qian, L and Yu, X and Huang, F and Hu, R and Su, H and Gu, H and Yan, Q and He, Z and Wang, C},
title = {The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes.},
journal = {Water research},
volume = {262},
number = {},
pages = {122113},
doi = {10.1016/j.watres.2024.122113},
pmid = {39032335},
issn = {1879-2448},
mesh = {*Denitrification ; *Nitrates/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Ammonium Compounds/metabolism ; Wetlands ; },
abstract = {Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining [15]N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4[+]. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.},
}
@article {pmid39029427,
year = {2024},
author = {Iacovacci, J and Serafini, MS and Avuzzi, B and Badenchini, F and Cicchetti, A and Devecchi, A and Dispinzieri, M and Doldi, V and Giandini, T and Gioscio, E and Mancinelli, E and Noris Chiorda, B and Orlandi, E and Palorini, F and Possenti, L and Reis Ferreira, M and Villa, S and Zaffaroni, N and De Cecco, L and Valdagni, R and Rancati, T},
title = {Intestinal microbiota composition is predictive of radiotherapy-induced acute gastrointestinal toxicity in prostate cancer patients.},
journal = {EBioMedicine},
volume = {106},
number = {},
pages = {105246},
pmid = {39029427},
issn = {2352-3964},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/radiation effects ; *Prostatic Neoplasms/radiotherapy ; Aged ; *Radiation Injuries/etiology/microbiology/diagnosis ; Middle Aged ; Metagenomics/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Radiotherapy/adverse effects ; Bacteria/classification/genetics/radiation effects ; Gastrointestinal Diseases/etiology/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy.<br><br>METHODS: Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology and the Ion Reporter metagenomic pipeline. Statistical techniques and computational and machine learning tools were used to extract, functionally characterise, and predict core features of the bacterial communities of patients who developed acute gastrointestinal toxicity.<br><br>FINDINGS: Analysis of the core bacterial composition in the discovery cohort revealed a cluster of patients significantly enriched for toxicity, displaying a toxicity rate of 60%. Based on selected high-risk microbiota compositional features, we developed a clinical decision tree that could effectively predict the risk of toxicity based on the relative abundance of genera Faecalibacterium, Bacteroides, Parabacteroides, Alistipes, Prevotella and Phascolarctobacterium both in internal and external validation cohorts.<br><br>INTERPRETATION: We provide evidence showing that intestinal bacteria profiling from baseline faecal samples can be effectively used in the clinic to improve the pre-radiotherapy assessment of gastrointestinal toxicity risk in prostate cancer patients.<br><br>FUNDING: Italian Ministry of Health (Promotion of Institutional Research INT-year 2016, 5 &#xd7; 1000, Ricerca Corrente funds). Fondazione Regionale per la Ricerca Biomedica (ID 2721017). AIRC (IG 21479).},
}
@article {pmid39111271,
year = {2024},
author = {Zhang, Y and Chen, W and Yuan, Y and Liao, X and Mi, J},
title = {Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175275},
doi = {10.1016/j.scitotenv.2024.175275},
pmid = {39111271},
issn = {1879-1026},
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Drug Resistance, Microbial/genetics ; Light ; Female ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.},
}
@article {pmid39094311,
year = {2024},
author = {Wang, X and Qian, Y and Wang, Y and Wang, S and Bi, J and Shi, C and Han, Q and Wan-Yan, R and Yu, Q and Li, H},
title = {Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135387},
doi = {10.1016/j.jhazmat.2024.135387},
pmid = {39094311},
issn = {1873-3336},
mesh = {Humans ; *Metagenomics ; Parks, Recreational ; Gastrointestinal Microbiome/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; China ; Bacteria/genetics/drug effects/classification ; Soil Microbiology ; Cities ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Genes, Bacterial ; },
abstract = {Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.},
}
@article {pmid39084364,
year = {2024},
author = {Kolenc, &#x17d; and Kovač Viršek, M and Klančnik, A and Janecko, N},
title = {Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175130},
doi = {10.1016/j.scitotenv.2024.175130},
pmid = {39084364},
issn = {1879-1026},
mesh = {Animals ; *Seawater/microbiology ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Slovenia ; *Microplastics/analysis ; *Environmental Monitoring ; Mytilus/microbiology ; Bacteria/classification/isolation &amp; purification ; },
abstract = {Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m[3] water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.},
}
@article {pmid39069186,
year = {2024},
author = {Zhu, S and Zhao, W and Sun, S and Yang, X and Mao, H and Sheng, L and Chen, Z},
title = {Community metagenomics reveals the processes of cadmium resistance regulated by microbial functions in soils with Oryza sativa root exudate input.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175015},
doi = {10.1016/j.scitotenv.2024.175015},
pmid = {39069186},
issn = {1879-1026},
mesh = {*Oryza/microbiology/physiology ; *Soil Microbiology ; *Cadmium ; *Soil Pollutants ; *Plant Roots/microbiology ; *Rhizosphere ; *Microbiota/drug effects ; Metagenomics ; Soil/chemistry ; },
abstract = {Plants exert a profound influence on their rhizosphere microbiome through the secretion of root exudates, thereby imparting critical effects on their growth and overall health. The results unveil that japonica rice showcases a remarkable augmentation in its antioxidative stress mechanisms under Cd stress. This augmentation is characterized by the sequestration of heavy metal ions within the root system and the prodigious secretion of a spectrum of flavonoids, including Quercetin, Luteolin, Apigenin, Kaempferide, and Sakuranetin. These flavonoids operate as formidable guardians, shielding the plant from oxidative damage instigated by Cd-induced stress. Furthermore, the metagenomic analyses divulge the transformative potential of flavonoids, as they induce profound alterations in the composition and structural dynamics of plant rhizosphere microbial communities. These alterations manifest through the recruitment of plant growth-promoting bacteria, effectively engineering a conducive milieu for japonica rice. In addition, our symbiotic network analysis discerns that flavonoid compounds significantly improved the positive correlations among dominant species within the rhizosphere of japonica rice. This, in turn, bolsters the stability and intricacy of the microenvironmental ecological network. KEGG functional analyses reveal a notable upregulation in the expression of flavonoid functional genes, specifically cadA, cznA, nccC, and czrB, alongside an array of transporters, encompassing RND, ABC, MIT, and P-ATPase. These molecular orchestrations distinctly demarcated the rhizosphere microbiome of japonica rice, markedly enhancing its tolerance to Cd-induced stress. These findings not only shed light on the establishment of Cd-resistant bacterial consortia in rice but also herald a promising avenue for the precise modulation of plant rhizosphere microbiomes, thereby fortifying the safety and efficiency of crop production.},
}
@article {pmid39069174,
year = {2024},
author = {Shu, D and Banerjee, S and Mao, X and Zhang, J and Cui, W and Zhang, W and Zhang, B and Chen, S and Jiao, S and Wei, G},
title = {Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174953},
doi = {10.1016/j.scitotenv.2024.174953},
pmid = {39069174},
issn = {1879-1026},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Nitrogen Cycle ; *Soil/chemistry ; *Nitrogen/metabolism ; *Agriculture/methods ; Glycine max/growth &amp; development ; Crop Production/methods ; },
abstract = {Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R[2] = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R[2] = 0.076 ~ R[2] = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.},
}
@article {pmid39068883,
year = {2024},
author = {Zhou, Z and Keiblinger, KM and Huang, Y and Bhople, P and Shi, X and Yang, S and Yu, F and Liu, D},
title = {Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135355},
doi = {10.1016/j.jhazmat.2024.135355},
pmid = {39068883},
issn = {1873-3336},
mesh = {*Manure/microbiology/virology ; *Composting ; *Streptomyces/genetics ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Virome/genetics ; Bacteria/drug effects/genetics ; Viruses/drug effects/genetics ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; },
abstract = {Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.},
}
@article {pmid39067601,
year = {2024},
author = {Roman, EKB and Ramos, MA and Tomazetto, G and Foltran, BB and Galvão, MH and Ciancaglini, I and Tramontina, R and de Almeida Rodrigues, F and da Silva, LS and Sandano, ALH and Fernandes, DGDS and Almeida, DV and Baldo, DA and de Oliveira Junior, JM and Garcia, W and Damasio, A and Squina, FM},
title = {Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174876},
doi = {10.1016/j.scitotenv.2024.174876},
pmid = {39067601},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; *Microbiota ; *Plastics/metabolism ; Soil Microbiology ; Polyethylene Terephthalates/metabolism ; Soil Pollutants/metabolism ; Polymers/metabolism ; Bacteria/metabolism/genetics ; Biodegradable Plastics/metabolism ; Microbial Consortia ; Pseudomonas putida/metabolism/genetics ; },
abstract = {Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.},
}
@article {pmid38986687,
year = {2024},
author = {Wang, J and Shen, C and Sun, J and Cheng, L and Zhao, G and Li, MM},
title = {Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174618},
doi = {10.1016/j.scitotenv.2024.174618},
pmid = {38986687},
issn = {1879-1026},
mesh = {*Rumen/microbiology/metabolism ; Animals ; *Animal Feed/analysis ; Gastrointestinal Microbiome ; Cattle ; Dietary Proteins/metabolism ; Fermentation ; Metagenomics ; Diet, Protein-Restricted ; Male ; Microbiota ; },
abstract = {Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.},
}
@article {pmid39147499,
year = {2024},
author = {Magliulo, R and Valentino, V and Balivo, A and Esposito, A and Genovese, A and Ercolini, D and De Filippis, F},
title = {Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114798},
doi = {10.1016/j.foodres.2024.114798},
pmid = {39147499},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; *Volatile Organic Compounds/analysis ; *Microbiota ; *Buffaloes ; Italy ; *Gas Chromatography-Mass Spectrometry ; *Taste ; Food Microbiology ; Lactobacillus helveticus ; Streptococcus thermophilus/classification ; },
abstract = {Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.},
}
@article {pmid39143364,
year = {2024},
author = {Akhlaghi, E and Salari, E and Mansouri, M and Shafiei, M and Kalantar-Neyestanaki, D and Aghassi, H and Fasihi Harandi, M},
title = {Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18912},
pmid = {39143364},
issn = {2045-2322},
support = {400000473//Kerman University of Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Echinococcosis, Hepatic/microbiology/parasitology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Feces/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.},
}
@article {pmid39059396,
year = {2024},
author = {Kim, Y and Kim, G and Kim, S and Cho, B and Kim, SY and Do, EJ and Bae, DJ and Kim, S and Kweon, MN and Song, JS and Park, SH and Hwang, SW and Kim, MN and Kim, Y and Min, K and Kim, SH and Adams, MD and Lee, C and Park, H and Park, SR},
title = {Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {8},
pages = {1380-1393.e9},
doi = {10.1016/j.chom.2024.06.010},
pmid = {39059396},
issn = {1934-6069},
mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Female ; Male ; Middle Aged ; *Neoplasms/immunology/therapy/microbiology ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Aged ; Feces/microbiology ; Adult ; Cytokines/metabolism ; },
abstract = {The gut microbiome significantly influences immune responses and the efficacy of immune checkpoint inhibitors. We conducted a clinical trial (NCT04264975) combining an anti-programmed death-1 (PD-1) inhibitor with fecal microbiota transplantation (FMT) from anti-PD-1 responder in 13 patients with anti-PD-1-refractory advanced solid cancers. FMT induced sustained microbiota changes and clinical benefits in 6 of 13 patients, with 1 partial response and 5 stable diseases, achieving an objective response rate of 7.7% and a disease control rate of 46.2%. The clinical response correlates with increased cytotoxic T cells and immune cytokines in blood and tumors. We isolated Prevotella merdae Immunoactis from a responder to FMT, which stimulates T cell activity and suppresses tumor growth in mice by enhancing cytotoxic T cell infiltration. Additionally, we found Lactobacillus salivarius and Bacteroides plebeius may inhibit anti-tumor immunity. Our findings suggest that FMT with beneficial microbiota can overcome resistance to anti-PD-1 inhibitors in advanced solid cancers, especially gastrointestinal cancers.},
}
@article {pmid38996548,
year = {2024},
author = {Wu, C and Yang, F and Zhong, H and Hong, J and Lin, H and Zong, M and Ren, H and Zhao, S and Chen, Y and Shi, Z and Wang, X and Shen, J and Wang, Q and Ni, M and Chen, B and Cai, Z and Zhang, M and Cao, Z and Wu, K and Gao, A and Li, J and Liu, C and Xiao, M and Li, Y and Shi, J and Zhang, Y and Xu, X and Gu, W and Bi, Y and Ning, G and Wang, W and Wang, J and Liu, R},
title = {Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {8},
pages = {1301-1314.e9},
doi = {10.1016/j.chom.2024.06.012},
pmid = {38996548},
issn = {1934-6069},
mesh = {*Inositol/metabolism ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Humans ; Mice ; Male ; Lipid Metabolism ; Female ; Intestinal Absorption ; Mice, Inbred C57BL ; Metagenomics ; Middle Aged ; Adult ; Fatty Acids/metabolism ; Escherichia coli/genetics/metabolism ; },
abstract = {Numerous studies have reported critical roles for the gut microbiota in obesity. However, the specific microbes that causally contribute to obesity and the underlying mechanisms remain undetermined. Here, we conducted shotgun metagenomic sequencing in a Chinese cohort of 631 obese subjects and 374 normal-weight controls and identified a Megamonas-dominated, enterotype-like cluster enriched in obese subjects. Among this cohort, the presence of Megamonas and polygenic risk exhibited an additive impact on obesity. Megamonas rupellensis possessed genes for myo-inositol degradation, as demonstrated in vitro and in vivo, and the addition of myo-inositol effectively inhibited fatty acid absorption in intestinal organoids. Furthermore, mice colonized with M. rupellensis or E. coli heterologously expressing the myo-inositol-degrading iolG gene exhibited enhanced intestinal lipid absorption, thereby leading to obesity. Altogether, our findings uncover roles for M. rupellensis as a myo-inositol degrader that enhances lipid absorption and obesity, suggesting potential strategies for future obesity management.},
}
@article {pmid38662518,
year = {2024},
author = {Lages da Silva, DH and Marques da Silva, RL and Rios, DL and de Souza, DDG and Aburjaile, F and de Freitas Neto, OC and Camargos Lara, LJ and Dias Araújo, M and Ecco, R},
title = {Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {53},
number = {5},
pages = {408-418},
doi = {10.1080/03079457.2024.2348509},
pmid = {38662518},
issn = {1465-3338},
mesh = {Animals ; *Chickens/microbiology/virology ; *Gastrointestinal Microbiome ; *Poultry Diseases/microbiology/virology ; *Metagenomics ; Brazil/epidemiology ; Dysbiosis/veterinary/microbiology ; Ileum/microbiology ; High-Throughput Nucleotide Sequencing/veterinary ; Growth Disorders/veterinary/microbiology ; Bacteria/isolation &amp; purification/classification/genetics ; },
abstract = {Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected or not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTS RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.},
}
@article {pmid38557867,
year = {2024},
author = {Bar Ziv, O and Cahn, A and Jansen, T and Istomin, V and Kedem, E and Olshtain-Pops, K and Israel, S and Oster, Y and Orenbuch-Harroch, E and Korem, M and Strahilevitz, J and Levy, I and Valdés-Mas, R and Ivanova, V and Elinav, E and Shahar, E and Elinav, H},
title = {Diagnosis and Risk Factors of Prediabetes and Diabetes in People Living With Human Immunodeficiency Virus: Evaluation of Clinical and Microbiome Parameters.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {2},
pages = {411-420},
doi = {10.1093/infdis/jiae167},
pmid = {38557867},
issn = {1537-6613},
support = {//D-cure/ ; //Novo Nordisk/ ; //Israeli HIV Association/ ; },
mesh = {Humans ; *Prediabetic State/diagnosis ; *HIV Infections/complications ; Female ; Male ; Middle Aged ; Risk Factors ; Prospective Studies ; Adult ; *Blood Glucose/analysis ; *Glycated Hemoglobin/analysis/metabolism ; *Microbiota ; *Diabetes Mellitus/epidemiology ; Glucose Tolerance Test ; },
abstract = {Diabetes mellitus (DM) is more common among people living with human immunodeficiency virus (PLWH) compared with healthy individuals. In a prospective multicenter study (N = 248), we identified normoglycemic (48.7%), prediabetic (44.4%), and diabetic (6.9%) PLWH. Glycosylated hemoglobin (HbA1c) and fasting blood glucose (FBG) sensitivity in defining dysglycemia was 96.8%, while addition of oral glucose tolerance test led to reclassification of only 4 patients. Inclusion of 93 additional PLWH with known DM enabled identification of multiple independent predictors of dysglycemia or diabetes: older age, higher body mass index, Ethiopian origin, HIV duration, lower integrase inhibitor exposure, and advanced disease at diagnosis. Shotgun metagenomic microbiome analysis revealed 4 species that were significantly expanded with hyperglycemia/hyperinsulinemia, and 2 species that were differentially more prevalent in prediabetic/diabetic PLWH. Collectively, we uncover multiple potential host and microbiome predictors of altered glycemic status in PLWH, while demonstrating that FBG and HbA1c likely suffice for diabetes screening. These potential diabetic predictors merit future prospective validation.},
}
@article {pmid39142773,
year = {2024},
author = {Zaytsev, V and Tutukina, MN and Chetyrkina, MR and Shelyakin, PV and Ovchinnikov, G and Satybaldina, D and Kondrashov, VA and Bandurist, MS and Seilov, S and Gorin, DA and Fedorov, FS and Gelfand, MS and Nasibulin, AG},
title = {Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities.},
journal = {Analytica chimica acta},
volume = {1320},
number = {},
pages = {343022},
doi = {10.1016/j.aca.2024.343022},
pmid = {39142773},
issn = {1873-4324},
mesh = {*Electronic Nose ; *Bacteria/isolation &amp; purification ; Meat/microbiology/analysis ; Microbiota ; Animals ; Food Quality ; Food Microbiology ; },
abstract = {BACKGROUND: Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.<br><br>RESULTS: We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R[2] values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.<br><br>SIGNIFICANCE: Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.},
}
@article {pmid39143178,
year = {2024},
author = {Duru, IC and Lecomte, A and Shishido, TK and Laine, P and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P},
title = {Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18906},
pmid = {39143178},
issn = {2045-2322},
support = {NNF22OC0080109//Novo Nordisk Foundation/ ; },
mesh = {*Parkinson Disease/genetics/microbiology ; Humans ; *Feces/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; Male ; Aged ; Female ; Genome, Microbial ; Middle Aged ; High-Throughput Nucleotide Sequencing ; },
abstract = {The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.},
}
@article {pmid39143108,
year = {2024},
author = {Grahnemo, L and Kambur, O and Lahti, L and Jousilahti, P and Niiranen, T and Knight, R and Salomaa, V and Havulinna, AS and Ohlsson, C},
title = {Associations between gut microbiota and incident fractures in the FINRISK cohort.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {69},
pmid = {39143108},
issn = {2055-5008},
support = {2020-01392//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; LU2021-0096//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; NNF 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; Female ; *Fractures, Bone/microbiology/epidemiology/etiology ; Middle Aged ; Finland/epidemiology ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Cohort Studies ; Incidence ; Metagenomics/methods ; Proteobacteria/genetics/isolation &amp; purification ; Risk Factors ; Adult ; },
abstract = {The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.},
}
@article {pmid39143045,
year = {2024},
author = {Baldi, A and Braat, S and Imrul Hasan, M and Bennett, C and Barrios, M and Jones, N and Moir-Meyer, G and Abdul Azeez, I and Wilcox, S and Saiful Alam Bhuiyan, M and Ataide, R and Clucas, D and Harrison, LC and Arifeen, SE and Bowden, R and Biggs, BA and Jex, A and Pasricha, SR},
title = {Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6980},
pmid = {39143045},
issn = {2041-1723},
support = {GNT1103262//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Bangladesh/epidemiology ; Infant ; *Anti-Bacterial Agents/administration &amp; dosage/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Administration, Oral ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Cephalosporins/administration &amp; dosage/pharmacology/therapeutic use ; Enterococcus/drug effects/genetics/isolation &amp; purification ; Antimicrobial Stewardship ; },
abstract = {Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.},
}
@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
doi = {10.1126/sciadv.adn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}
@article {pmid39140734,
year = {2024},
author = {Tian, Y and Rimal, B and Bisanz, JE and Gui, W and Wolfe, TM and Koo, I and Murray, IA and Nettleford, SK and Yokoyama, S and Dong, F and Koshkin, S and Prabhu, KS and Turnbaugh, PJ and Walk, ST and Perdew, GH and Patterson, AD},
title = {Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.},
journal = {Environmental health perspectives},
volume = {132},
number = {8},
pages = {87005},
doi = {10.1289/EHP13356},
pmid = {39140734},
issn = {1552-9924},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; *Mice, Inbred C57BL ; *Homeostasis/drug effects ; *Benzofurans ; Persistent Organic Pollutants ; Male ; Ligands ; },
abstract = {BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship.<br><br>OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life.<br><br>METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics.<br><br>RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway.<br><br>CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.},
}
@article {pmid39140417,
year = {2024},
author = {Hummel, G and Aagaard, K},
title = {Arthropods to Eutherians: A Historical and Contemporary Comparison of Sparse Prenatal Microbial Communities Among Animalia Species.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {92},
number = {2},
pages = {e13897},
doi = {10.1111/aji.13897},
pmid = {39140417},
issn = {1600-0897},
mesh = {Animals ; Humans ; *Microbiota ; Pregnancy ; Female ; },
abstract = {Since the advent of next-generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia.},
}
@article {pmid39138568,
year = {2024},
author = {Belda, E and Capeau, J and Zucker, JD and Chatelier, EL and Pons, N and Oñate, FP and Quinquis, B and Alili, R and Fellahi, S and Katlama, C and Clément, K and Fève, B and Jaureguiberry, S and Goujard, C and Lambotte, O and Doré, J and Prifti, E and Bastard, JP},
title = {Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {209},
pmid = {39138568},
issn = {1755-8794},
support = {ANRS 157 study trial//Agence Nationale de Recherches sur le Sida et les H&#xe9;patites Virales/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Male ; Female ; Middle Aged ; *Insulin Resistance ; Adult ; Feces/microbiology ; Anti-Retroviral Agents/therapeutic use ; Metagenome ; },
abstract = {BACKGROUND: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated.<br><br>METHODS: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc.<br><br>RESULTS: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc.<br><br>CONCLUSION: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.},
}
@article {pmid39136189,
year = {2024},
author = {Wang, J and Zhu, YG and Ge, Y},
title = {Global distribution pattern of soil phosphorus-cycling microbes under the influence of human activities.},
journal = {Global change biology},
volume = {30},
number = {8},
pages = {e17477},
doi = {10.1111/gcb.17477},
pmid = {39136189},
issn = {1365-2486},
support = {2023YFD1700803//National Key Research and Development Program of China/ ; 42177274//National Natural Science Foundation of China/ ; 42307162//National Natural Science Foundation of China/ ; 2019QZKK0306//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0308//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Phosphorus/metabolism/analysis ; *Soil Microbiology ; Human Activities ; Humans ; Bacteria/genetics/metabolism ; Microbiota ; Soil/chemistry ; },
abstract = {Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle.},
}
@article {pmid38981389,
year = {2024},
author = {Li, W and Wang, Y and Gao, J and Wang, A},
title = {Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau.},
journal = {Ecotoxicology and environmental safety},
volume = {282},
number = {},
pages = {116699},
doi = {10.1016/j.ecoenv.2024.116699},
pmid = {38981389},
issn = {1090-2414},
mesh = {*Wetlands ; Risk Assessment ; Tibet ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Drug Resistance, Bacterial/genetics ; China ; Bacteria/genetics/drug effects/classification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; Interspersed Repetitive Sequences ; },
abstract = {Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.},
}
@article {pmid38980039,
year = {2024},
author = {Su, L and Marshall, IPG and Teske, AP and Yao, H and Li, J},
title = {Genomic characterization of the bacterial phylum Candidatus Effluviviacota, a cosmopolitan member of the global seep microbiome.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0099224},
doi = {10.1128/mbio.00992-24},
pmid = {38980039},
issn = {2150-7511},
support = {42072333//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021YFF0501301//MOST | National Key Research and Development Program of China (NKPs)/ ; //Shanghai Pilot Program for Basic Research/ ; OCE-0647633//NSF-OCE/ ; },
mesh = {*Phylogeny ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; *Genome, Bacterial ; *Geologic Sediments/microbiology ; *Metagenome ; Seawater/microbiology ; Metagenomics ; },
abstract = {UNLABELLED: The microbial communities of marine seep sediments contain unexplored physiological and phylogenetic diversity. Here, we examined 30 bacterial metagenome-assembled genomes (MAGs) from cold seeps in the South China Sea, the Indian Ocean, the Scotian Basin, and the Gulf of Mexico, as well as from deep-sea hydrothermal sediments in the Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct phylum-level bacterial lineage, which we propose as a new phylum, Candidatus Effluviviacota, in reference to its preferential occurrence at diverse seep areas. Based on tightly clustered high-quality MAGs, we propose two new genus-level candidatus taxa, Candidatus Effluvivivax and Candidatus Effluvibates. Genomic content analyses indicate that Candidatus Effluviviacota are chemoheterotrophs that harbor the Embden-Meyerhof-Parnas glycolysis pathway. They gain energy by fermenting organic substrates. Additionally, they display potential capabilities for the degradation of cellulose, hemicellulose, starch, xylan, and various peptides. Extracellular anaerobic respiration appears to rely on metals as electron acceptors, with electron transfer primarily mediated by multiheme cytochromes and by a flavin-based extracellular electron transfer (EET) mechanism that involves NADH-quinone oxidoreductase-demethylmenaquinone-synthesizing enzymes, uncharacterized membrane proteins, and flavin-binding proteins, also known as the NUO-DMK-EET-FMN complex. The heterogeneity within the Ca. Effluviviacota phylum suggests varying roles in energy metabolism among different genera. While NUO-DMK-EET-FMN electron transfer has been reported predominantly in Gram-positive bacteria, it is now identified in Ca. Effluviviacota as well. We detected the presence of genes associated with bacterial microcompartments in Ca. Effluviviacota, which can promote specific metabolic processes and protect the cytosol from toxic intermediates.<br><br>IMPORTANCE: The newly discovered bacterial phylum Candidatus Effluviviacota is widespread across diverse seepage ecosystems, marine environments, and freshwater environments, with a notable preference for cold seeps. While maintaining an average abundance of approximately 1% in the global gene catalog of cold seep habitats, it has not hitherto been characterized. The metabolic versatility of Ca. Effluviviacota in anaerobic carbon, hydrogen, and metal cycling aligns with its prevalence in anoxic niches, with a preference for cold seep environments. Variations in metabolic potential between Ca. Effluvivivax and Ca. Effluvibates may contribute to shaping their respective habitat distributions.},
}
@article {pmid39134593,
year = {2024},
author = {Trosvik, P and Noordzij, HT and de Muinck, EJ},
title = {Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18701},
pmid = {39134593},
issn = {2045-2322},
support = {300948//Norges Forskningsr&#xe5;d/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenomics/methods ; Metagenome ; Genes, Bacterial ; Bacteria/genetics/classification ; Infant, Newborn ; Female ; },
abstract = {Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.},
}
@article {pmid39080826,
year = {2024},
author = {Lee, JY and Choi, M and Song, MJ and Kim, DD and Yun, T and Chang, J and Ho, A and Myung, J and Yoon, S},
title = {Selective Enrichment of Methylococcaceae versus Methylocystaceae Methanotrophs via Control of Methane Feeding Schemes.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {32},
pages = {14237-14248},
doi = {10.1021/acs.est.4c02655},
pmid = {39080826},
issn = {1520-5851},
mesh = {*Methane/metabolism ; *Methylococcaceae/metabolism ; *Methylocystaceae/metabolism ; Soil Microbiology ; Microbiota ; },
abstract = {Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, the contributions of different groups of methanotrophs at terrestrial CH4-oxidation hotspots, such as the oxic-anoxic interface of rice paddies, have shown considerable inconsistency across observations. To address the knowledge gap regarding this inconsistency, methanotrophic microbiomes were enriched from paddy soils in well-mixed CH4-fed batch reactors under six different incubation conditions, prepared as combinations of two CH4 mixing ratios (0.5 and 10%) and three supplemented Cu[2+] concentrations (0, 2, and 10 μM). Monitoring of temporal community shifts in these cultures revealed a dominance of Methylocystis spp. in all 0.5%-CH4 cultures, while methanotrophs affiliated to Gammaproteobacteria dominated the 10%-CH4 cultures that were less consistent both temporally and across conditions. The shotgun metagenome analyses of the 0.5%-CH4 cultures corroborated the Methylocystis dominance and, interestingly, showed that copper deficiency did not select for mmoXYZ-possessing methanotrophs. Instead, a mbn cluster, accounting for approximately 5% of the Methylocystis population, was identified, suggesting the ecological significance of methanobactin in Cu-deficient methanotrophy. These findings underscore the important role of Methylocystis spp. in mitigating emissions from terrestrial CH4 hotspots and suggest the feasibility of directed enrichment and/or isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production.},
}
@article {pmid39067396,
year = {2024},
author = {Xie, XM and Feng, S and Liu, T and Feng, J and Xu, Y and Fan, ZJ and Wang, GY},
title = {Role of gut/liver metabolites and gut microbiota in liver fibrosis caused by cholestasis.},
journal = {International immunopharmacology},
volume = {139},
number = {},
pages = {112747},
doi = {10.1016/j.intimp.2024.112747},
pmid = {39067396},
issn = {1878-1705},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Cholestasis/metabolism/pathology/microbiology ; *Liver Cirrhosis/metabolism/microbiology/pathology ; Mice ; *Liver/metabolism/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Metabolomics ; },
abstract = {AIM OF THE STUDY: Cholestasis induces severe liver injury and subsequent liver fibrosis. However, a comprehensive understanding of the relationships between liver fibrosis and cholestasis-induced changes in metabolites in the gut and fibrotic liver tissue and in the gut microbiota is insufficient.<br><br>METHODS: Common bile duct ligation (BDL) was employed to establish a cholestatic liver fibrosis model in mice for 26&#xa0;days. Fibrotic liver tissue and the gut contents were collected. Untargeted metabolomics was conducted for the determination of metabolites in the gut contents and liver tissues. Metagenomics was adopted to explore the gut microbiota.<br><br>RESULTS: The metabolites in the gut contents and liver tissues between normal and cholestatic liver fibrosis mice were highly distinct. Beta-alanine metabolism and glutathione metabolism were downregulated in the gut of the BDL group. Galactose metabolism, biosynthesis of unsaturated fatty acids, and ABC transporters were upregulated in the gut and downregulated in the liver of the BDL group. Arginine biosynthesis, taurine and hypotaurine metabolism, arginine and proline metabolism, and primary bile acid biosynthesis were downregulated in the gut and upregulated in the liver of the BDL group. Metagenomic analysis revealed that the alpha diversity of the microbiota in the BDL group decreased. The altered structure of the gut microbiota in the BDL group led to the hypofunction of important metabolic pathways (such as folate biosynthesis, histidine metabolism, thiamine metabolism, biotin metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis) and enzymes (such as NADH, DNA helicase, and DNA-directed DNA polymerase). Correlation analyses indicated that certain gut microbes were associated with gut and liver metabolites.<br><br>CONCLUSIONS: Untargeted metabolomics and metagenomics provided comprehensive information on gut and liver metabolism and gut microbiota in mice with cholestatic liver fibrosis. Therefore, significantly altered bacteria and metabolites may help provide some targets against cholestatic liver fibrosis in the future.},
}
@article {pmid37365419,
year = {2024},
author = {Gryaznova, M and Smirnova, Y and Burakova, I and Syromyatnikov, M and Chizhkov, P and Popov, E and Popov, V},
title = {Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People.},
journal = {Probiotics and antimicrobial proteins},
volume = {16},
number = {4},
pages = {1240-1250},
pmid = {37365419},
issn = {1867-1314},
support = {FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/administration &amp; dosage ; *Lactobacillales/physiology/classification ; Adult ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Young Adult ; },
abstract = {The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.},
}
@article {pmid39133323,
year = {2024},
author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG},
title = {Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {438},
pmid = {39133323},
issn = {1432-0614},
support = {Project Reference No: BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Plant Leaves ; *Moringa/chemistry ; Sheep ; *Feces/microbiology ; *Goats ; Dietary Supplements ; Fatty Acids, Volatile/metabolism ; Rumen/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Weight Gain/drug effects ; Diet/veterinary ; Metagenomics ; },
abstract = {This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.},
}
@article {pmid39128916,
year = {2024},
author = {Osburn, ED and McBride, SG and Bahram, M and Strickland, MS},
title = {Global patterns in the growth potential of soil bacterial communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6881},
pmid = {39128916},
issn = {2041-1723},
support = {2020-67034-41310//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2021-03724//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 1845417//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/growth &amp; development/metabolism ; *Soil/chemistry ; *Ecosystem ; *Carbon/metabolism ; Nitrogen/metabolism ; Metagenome ; Forests ; Carbon Cycle ; Microbiota ; Codon Usage ; },
abstract = {Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.},
}
@article {pmid39033587,
year = {2024},
author = {Pavon, JAR and da Silva Neves, NA and Pinho, JB and de Souza, VJ and Patroca da Silva, S and Ribeiro Cruz, AC and de Almeida Medeiros, DB and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019.},
journal = {Virology},
volume = {598},
number = {},
pages = {110182},
doi = {10.1016/j.virol.2024.110182},
pmid = {39033587},
issn = {1096-0341},
mesh = {Animals ; Brazil ; Female ; *Anopheles/virology ; *Virome/genetics ; *Phylogeny ; *Aedes/virology ; *Culex/virology ; *Genome, Viral ; Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; Insect Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.},
}
@article {pmid39023128,
year = {2024},
author = {Li, L and Sun, H and Tan, L and Guo, H and He, L and Chen, J and Chen, S and Liu, D and Zhu, M and OuYang, Z},
title = {Miao sour soup alleviates DSS-induced colitis in mice: modulation of gut microbiota and intestinal barrier function.},
journal = {Food &amp; function},
volume = {15},
number = {16},
pages = {8370-8385},
doi = {10.1039/d4fo01794c},
pmid = {39023128},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced ; *Dextran Sulfate/adverse effects ; Male ; *Intestinal Mucosa/microbiology ; Mice, Inbred C57BL ; Fermented Foods ; Disease Models, Animal ; Colon/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/isolation &amp; purification/genetics ; Intestinal Barrier Function ; },
abstract = {Miao sour soup (MSS), a daily fermented food in Guizhou, China, is rich in microorganisms with various beneficial activities, including anti-inflammatory and antioxidant activities. However, the therapeutic effects of MSS on IBD remain unexplored. This study aimed to investigate the protective effect of MSS against colitis in mice. In this study, we examined the microbial community structure of MSS by metagenomic sequencing and also explored the protective effect of MSS on DSS-induced colitis in mice. We investigated the effects of MSS on intestinal inflammatory response and intestinal barrier function in mice. Finally, the changes in intestinal flora were analyzed based on the 16S rRNA gene sequencing results. Significantly, the experiment result shows that MSS ameliorated the severity of DSS-induced disease in mice by mitigating colitis-associated weight loss, reducing the disease activity index of IBD, alleviating colonic hemorrhagic lesions, increasing colon length, and improving colonic tissue damage. Moreover, MSS preserved intestinal barrier integrity and restored intestinal epithelial function in mice. Additionally, MSS modulated the structure and composition of the intestinal flora. Furthermore, MSS downregulated pro-inflammatory factors and attenuated the NF-κB p65 expression, thereby mitigating the inflammatory response. These findings highlight the protective effect of MSS against DSS-induced colitis, providing substantial scientific support for potential applications of MSS as a functional food.},
}
@article {pmid38906446,
year = {2024},
author = {Ran, Z and Yang, J and Liu, L and Wu, S and An, Y and Hou, W and Cheng, T and Zhang, Y and Zhang, Y and Huang, Y and Zhang, Q and Wan, J and Li, X and Xing, B and Ye, Y and Xu, P and Chen, Z and Zhao, J and Li, R},
title = {Chronic PM2.5 exposure disrupts intestinal barrier integrity via microbial dysbiosis-triggered TLR2/5-MyD88-NLRP3 inflammasome activation.},
journal = {Environmental research},
volume = {258},
number = {},
pages = {119415},
doi = {10.1016/j.envres.2024.119415},
pmid = {38906446},
issn = {1096-0953},
mesh = {Animals ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; *Dysbiosis/chemically induced ; *Inflammasomes/metabolism/drug effects ; *Mice, Inbred C57BL ; *Particulate Matter/toxicity ; *Myeloid Differentiation Factor 88/metabolism/genetics ; *Toll-Like Receptor 2/metabolism ; Mice ; *Toll-Like Receptor 5/metabolism ; Air Pollutants/toxicity ; Male ; Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/metabolism/drug effects ; Intestines/drug effects/microbiology ; },
abstract = {BACKGROUND: PM2.5, a known public health risk, is increasingly linked to intestinal disorders, however, the mechanisms of its impact are not fully understood.<br><br>PURPOSE: This study aimed to explore the impact of chronic PM2.5 exposure on intestinal barrier integrity and to uncover the underlying molecular mechanisms.<br><br>METHODS: C57BL/6&#xa0;J mice were exposed to either concentrated ambient PM2.5 (CPM) or filtered air (FA) for six months to simulate urban pollution conditions. We evaluated intestinal barrier damage, microbial shifts, and metabolic changes through histopathology, metagenomics, and metabolomics. Analysis of the TLR signaling pathway was also conducted.<br><br>RESULTS: The mean concentration of PM2.5 in the CPM exposure chamber was consistently measured at 70.9&#xa0;&#xb1;&#xa0;26.8&#xa0;&#x3bc;g/m&#xb3; throughout the study period. Our findings show that chronic CPM exposure significantly compromises intestinal barrier integrity, as indicated by reduced expression of the key tight junction proteins Occludin and Tjp1/Zo-1. Metagenomic sequencing revealed significant shifts in the microbial landscape, identifying 35 differentially abundant species. Notably, there was an increase in pro-inflammatory nongastric Helicobacter species and a decrease in beneficial bacteria, such as Lactobacillus intestinalis, Lactobacillus sp. ASF360, and Eubacterium rectale. Metabolomic analysis further identified 26 significantly altered metabolites commonly associated with intestinal diseases. A strong correlation between altered bacterial species and metabolites was also observed. For example, 4 Helicobacter species all showed positive correlations with 13 metabolites, including Lactate, Bile acids, Pyruvate and Glutamate. Additionally, increased expression levels of TLR2, TLR5, Myd88, and NLRP3 proteins were noted, and their expression patterns showed a strong correlation, suggesting a possible involvement of the TLR2/5-MyD88-NLRP3 signaling pathway.<br><br>CONCLUSIONS: Chronic CPM exposure induces intestinal barrier dysfunction, microbial dysbiosis, metabolic imbalance, and activation of the TLR2/5-MyD88-NLRP3 inflammasome. These findings highlight the urgent need for intervention strategies to mitigate the detrimental effects of air pollution on intestinal health and identify potential therapeutic targets.},
}
@article {pmid38906444,
year = {2024},
author = {Asif, A and Koner, S and Chen, JS and Hussain, A and Huang, SW and Hussain, B and Hsu, BM},
title = {Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality.},
journal = {Environmental research},
volume = {258},
number = {},
pages = {119457},
doi = {10.1016/j.envres.2024.119457},
pmid = {38906444},
issn = {1096-0953},
mesh = {*Trichloroethylene/metabolism ; *Biodegradation, Environmental ; *Microbiota ; Volcanic Eruptions ; Bacteria/genetics/metabolism/classification ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.},
}
@article {pmid39127849,
year = {2024},
author = {Vigil, BE and Ascue, F and Ayala, RY and Murúa, P and Calderon, MS and Bustamante, DE},
title = {Functional prediction based on 16S rRNA metagenome data from bacterial microbiota associated with macroalgae from the Peruvian coast.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18577},
pmid = {39127849},
issn = {2045-2322},
support = {Project FitoAlga N&#xb0; PE501079919-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; },
mesh = {*Seaweed/microbiology ; *RNA, Ribosomal, 16S/genetics ; Peru ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Macroalgae are vital reservoirs for essential epibiotic microorganisms. Among these are growth-promoting bacteria that support the growth and healthy development of their host macroalgae, and these macroalgae can be utilized in agriculture as biostimulants, offering an alternative to traditional agrochemicals. However, to date, no comparative studies have been conducted on the functional profile and bacterial diversity associated with coastal macroalgae of Peru. In this study, we employed amplicon sequencing of the V3-V4 region of 16S rRNA gene in twelve host macroalgae collected from two rocky shores in central Peru to compare their bacterial communities. The results revealed high bacterial diversity across both sites, but differences in microbial composition were noted. The phyla Bacteroidota and Pseudomonadota were predominant. The functional prediction highlighted 44 significant metabolic pathways associated with the bacterial microbiota when comparing host macroalgae. These active pathways are related to metabolism and genetic and cellular information processing. No direct association was detected between the macroalgal genera and the associated microbiota, suggesting that the bacterial community is largely influenced by their genetic functions than the taxonomic composition of their hosts. Furthermore, some species of Chlorophyta and Rhodophyta were observed to host growth-promoting bacteria, such as Maribacter sp. and Sulfitobacter sp.},
}
@article {pmid39127718,
year = {2024},
author = {Van Uffelen, A and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K},
title = {Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {864},
pmid = {39127718},
issn = {2052-4463},
mesh = {*Metagenomics/methods ; *Benchmarking ; *Bacteria/genetics/classification ; Nanopore Sequencing ; Nanopores ; Microbiota ; },
abstract = {Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.},
}
@article {pmid39125688,
year = {2024},
author = {Ercolano, C and Iacono, R and Cafaro, V and Pizzo, E and Giovannelli, D and Feuerriegel, G and Streit, WR and Strazzulli, A and Moracci, M},
title = {Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125688},
issn = {1422-0067},
support = {2020SBNHLH_003//Ministero dell'Universit&#xe0; e della Ricerca (MUR)/ ; },
mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Hydrolysis ; *Enzyme Stability ; Phylogeny ; Temperature ; Substrate Specificity ; Kinetics ; Hydrolases/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism/genetics ; },
abstract = {Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.},
}
@article {pmid38884260,
year = {2024},
author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC},
title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.},
journal = {Nucleic acids research},
volume = {52},
number = {14},
pages = {e61},
doi = {10.1093/nar/gkae515},
pmid = {38884260},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Colorectal Neoplasms/genetics/microbiology ; Diarrhea/microbiology/genetics ; Bacteria/genetics/classification ; },
abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.},
}
@article {pmid38821186,
year = {2024},
author = {Xu, Q and Mei, Z and Zha, Q and Chen, J and Qin, H and Liu, B and Jie, Z and Wu, X},
title = {Characterization of bronchoalveolar lavage fluid microbiota in acute exacerbations of bronchiectasis with non-tuberculous mycobacterial detection.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {146},
number = {},
pages = {107120},
doi = {10.1016/j.ijid.2024.107120},
pmid = {38821186},
issn = {1878-3511},
mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Microbiota ; *Nontuberculous Mycobacteria/isolation &amp; purification/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; High-Throughput Nucleotide Sequencing ; Community-Acquired Infections/microbiology/diagnosis ; },
abstract = {OBJECTIVES: Non-tuberculous mycobacteria (NTM) frequently colonize the airways of patients with bronchiectasis; however, there has been limited research into airway microbiota composition and predisposing factors for NTM detection during acute bronchiectasis exacerbations.<br><br>METHODS: This study enrolled 34 patients with bronchiectasis experiencing acute exacerbations. Metagenomic next-generation sequencing was used to detect microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used for the comparative analysis of meaningful microbiota in the BALF of patients with acute exacerbations of bronchiectasis. A correlation analysis was conducted to identify susceptibility factors for NTM in patients with bronchiectasis.<br><br>RESULTS: Compared with patients with community-acquired pneumonia, patients with bronchiectasis had higher detection rates of NTM (38.2%), Pseudomonas aeruginosa, and Haemophilus influenzae. Patients with NTM-positive bronchiectasis had lower body mass index and lipid profiles than patients who were NTM-negative. Metagenomic next-generation sequencing of BALF revealed patients who were NTM-positive had increased relative abundance of Rothia and other anaerobic genera compared with patients who were NTM-negative. Patients who were NTM-positive also showed higher levels of Streptococcus parasanguinis at the species level. Elevated Rothia mucilaginosa and S. parasanguinis correlated with decreased percentages of clusters of differentiation 3+ T lymphocytes and clusters of differentiation 3+ T-cell subgroups in peripheral blood.<br><br>CONCLUSIONS: NTM colonization increases the risk of acute bronchiectasis exacerbations. Low body mass index, lipid levels, and isolation of R. mucilaginosa and S. parasanguinis in BALF are susceptibility factors for NTM colonization in patients with bronchiectasis.},
}
@article {pmid37754684,
year = {2023},
author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH},
title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0022623},
pmid = {37754684},
issn = {2165-0497},
support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; },
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.},
}
@article {pmid37695074,
year = {2023},
author = {Park, H and Lim, SJ and Cosme, J and O'Connell, K and Sandeep, J and Gayanilo, F and Cutter, GR and Montes, E and Nitikitpaiboon, C and Fisher, S and Moustahfid, H and Thompson, LR},
title = {Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0523722},
pmid = {37695074},
issn = {2165-0497},
support = {NA21OAR4320190//National Oceanic and Atmospheric Administration/ ; NA20OAR4320472//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; },
mesh = {*Metagenome ; *Machine Learning ; *Metagenomics/methods ; *Algorithms ; Seawater/microbiology ; Microbiota/genetics ; Aquatic Organisms/classification/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Deep Learning ; },
abstract = {Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.},
}
@article {pmid39125621,
year = {2024},
author = {Jelin-Uhlig, S and Weigel, M and Ott, B and Imirzalioglu, C and Howaldt, HP and Böttger, S and Hain, T},
title = {Bisphosphonate-Related Osteonecrosis of the Jaw and Oral Microbiome: Clinical Risk Factors, Pathophysiology and Treatment Options.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
doi = {10.3390/ijms25158053},
pmid = {39125621},
issn = {1422-0067},
support = {DZIF-MD / 80325MD058//German Center for Infection Research/ ; },
mesh = {Humans ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/etiology/microbiology ; *Microbiota/drug effects ; Risk Factors ; *Diphosphonates/adverse effects/therapeutic use ; Mouth/microbiology ; },
abstract = {Bisphosphonate-related osteonecrosis of the jaw (BRONJ) represents a serious health condition, impacting the lives of many patients worldwide. The condition challenges clinical care due to its complex etiology and limited therapeutic options. A thorough understanding of the pathophysiological and patient-related factors that promote disease development is essential. Recently, the oral microbiome has been implicated as a potential driver and modulating factor of BRONJ by several studies. Modern genomic sequencing methods have provided a wealth of data on the microbial composition of BRONJ lesions; however, the role of individual species in the process of disease development remains elusive. A comprehensive PubMed search was conducted to identify relevant studies on the microbiome of BRONJ patients using the terms "microbiome", "osteonecrosis of the jaws", and "bisphosphonates". Studies focusing on symptoms, epidemiology, pathophysiology, risk factors, and treatment options were included. The principal risk factors for BRONJ are tooth extraction, surgical procedures, and the administration of high doses of bisphosphonates. Importantly, the oral microbiome plays a significant role in the progression of the disease. Several studies have identified alterations of microbial composition in BRONJ lesions. However, there is no consensus regarding bacterial species that are associated with BRONJ across studies. The bacterial genera typically found include Actinomyces, Fusobacterium, and Streptococcus. It is postulated that these microbes contribute to the pathogenesis of BRONJ by promoting inflammation and disrupting normal bone remodeling processes. Current therapeutic approaches are disease-stage-specific and the necessity for more effective treatment strategies remains. This review examines the potential causes of and therapeutic approaches to BRONJ, highlighting the link between microbial colonization and BRONJ development. Future research should seek to more thoroughly investigate the interactions between bisphosphonates, the oral microbiome, and the immune system in order to develop targeted therapies.},
}
@article {pmid39125593,
year = {2024},
author = {Kulecka, M and Czarnowski, P and Bałabas, A and Turkot, M and Kruczkowska-Tarantowicz, K and Żeber-Lubecka, N and Dąbrowska, M and Paszkiewicz-Kozik, E and Walewski, J and Ługowska, I and Koseła-Paterczyk, H and Rutkowski, P and Kluska, A and Piątkowska, M and Jagiełło-Gruszfeld, A and Tenderenda, M and Gawiński, C and Wyrwicz, L and Borucka, M and Krzakowski, M and Zając, L and Kamiński, M and Mikula, M and Ostrowski, J},
title = {Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
doi = {10.3390/ijms25158026},
pmid = {39125593},
issn = {1422-0067},
support = {2017/27/B/NZ5/01504//National Science Center/ ; 2018/31/B/NZ7/02675//National Science Center/ ; 2020/ABM/01/00004//The Medical Research Agency/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology ; Male ; *Formates/metabolism ; Middle Aged ; Aged ; Neoplasms/metabolism/microbiology ; Adult ; Dysbiosis/microbiology ; Metabolomics/methods ; Metabolome ; Gas Chromatography-Mass Spectrometry ; Metagenomics/methods ; },
abstract = {The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.},
}
@article {pmid39123130,
year = {2024},
author = {Bak, F and Keuschnig, C and Nybroe, O and Aamand, J and Jørgensen, PR and Nicolaisen, MH and Vogel, TM and Larose, C},
title = {Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {296},
pmid = {39123130},
issn = {1471-2180},
mesh = {*Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Archaea/genetics/classification/metabolism ; *Fungi/genetics/classification/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Soil Microbiology ; Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Clay ; Sequence Analysis, DNA ; Ecosystem ; Soil/chemistry ; },
abstract = {BACKGROUND: Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.<br><br>RESULTS: The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150&#xa0;cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150&#xa0;cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.<br><br>CONCLUSIONS: Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.},
}
@article {pmid39122767,
year = {2024},
author = {Zhang, B and Magnaye, KM and Stryker, E and Moltzau-Anderson, J and Porsche, CE and Hertz, S and McCauley, KE and Smith, BJ and Zydek, M and Pollard, KS and Ma, A and El-Nachef, N and Lynch, SV},
title = {Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18558},
pmid = {39122767},
issn = {2045-2322},
support = {T32 DK007007/DK/NIDDK NIH HHS/United States ; K12 GM081266-11/GM/NIGMS NIH HHS/United States ; 1563159//National Science Foundation/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/therapy/metabolism ; *Fecal Microbiota Transplantation ; Male ; Female ; *Feces/microbiology ; *Bacteroides/genetics ; Adult ; *Intestinal Mucosa/microbiology/metabolism ; Middle Aged ; Gastrointestinal Microbiome ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metabolome ; },
abstract = {Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n = 38) and fecal samples (n = 179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (≥ 3 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.},
}
@article {pmid39122705,
year = {2024},
author = {Neshat, SA and Santillan, E and Seshan, H and Wuertz, S},
title = {Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {855},
pmid = {39122705},
issn = {2052-4463},
mesh = {*Sewage/microbiology ; *Metagenome ; *Bioreactors ; Metagenomics ; Microbiota ; },
abstract = {Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.},
}
@article {pmid39118486,
year = {2024},
author = {Cui, S and Guo, R and Chen, C and Zhang, Y and Meng, J and Liu, L and Li, Y and Kang, Z and Li, S and Yan, Q and Ma, Y},
title = {Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia.},
journal = {Influenza and other respiratory viruses},
volume = {18},
number = {8},
pages = {e13362},
pmid = {39118486},
issn = {1750-2659},
support = {81902037//National Natural Science Foundation of China/ ; 20180550075//Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {Humans ; *Virome ; *High-Throughput Nucleotide Sequencing ; Child, Preschool ; *Nasopharynx/virology/microbiology ; *Bronchoalveolar Lavage Fluid/virology/microbiology ; Male ; Female ; Infant ; *Viruses/isolation &amp; purification/genetics/classification ; Child ; Oropharynx/virology/microbiology ; Pneumonia/microbiology/virology/diagnosis ; Metagenomics/methods ; },
abstract = {BACKGROUND: Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce.<br><br>METHODS: We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia.<br><br>RESULTS: Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing.<br><br>CONCLUSIONS: This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.},
}
@article {pmid39117774,
year = {2024},
author = {Durand, K and Yainna, S and Nam, K},
title = {Population genomics unravels a lag phase during the global fall armyworm invasion.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {957},
pmid = {39117774},
issn = {2399-3642},
mesh = {Animals ; *Introduced Species ; *Spodoptera/genetics ; Genetic Variation ; Gene Flow ; Genetics, Population ; Metagenomics ; Genomics/methods ; },
abstract = {The time that elapsed between the initial introduction and the proliferation of an invasive species is referred to as the lag phase. The identification of the lag phase is critical for generating plans for pest management and for the prevention of biosecurity failure. However, lag phases have been identified mostly through retrospective searches of historical records. The agricultural pest fall armyworm (FAW; Spodoptera frugiperda) is native to the New World. FAW invasion was first reported from West Africa in 2016, then it spread quickly through Africa, Asia, and Oceania. Here, using population genomics approaches, we demonstrate that the FAW invasion involved an undocumented lag phase. Invasive FAW populations have negative signs of genomic Tajima's D, and invasive population-specific genetic variations have particularly decreased Tajima's D, supporting a substantial amount of time for the generation of new mutations in introduced FAW populations. Model-based diffusion approximations support the existence of a period with a cessation of gene flow between native and invasive FAW populations. Taken together, these results provide strong support for the presence of a lag phase during the FAW invasion. These results show the usefulness of using population genomics analyses to identify lag phases in biological invasions.},
}
@article {pmid38775898,
year = {2024},
author = {Ferrarezi, JVS and Owatari, MS and Martins, MA and de Souza Sá, L and Dutra, SAP and de Oliveira, HM and Soligo, T and Martins, ML and Mouriño, JLP},
title = {Effects of a multi-strain Bacillus probiotic on the intestinal microbiome, haemato-immunology, and growth performance of Nile tilapia.},
journal = {Veterinary research communications},
volume = {48},
number = {4},
pages = {2357-2368},
pmid = {38775898},
issn = {1573-7446},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 301524/2017-3; 306635/2018-6 and 155524/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Cichlids/immunology/growth &amp; development/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bacillus ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; },
abstract = {The study evaluated dietary supplementation with a feed additive composed of multi-strain Bacillus for Nile tilapia Oreochromis niloticus. In vitro and in vivo assays employing culture-based microbiological methods and metagenomics were performed. Additionally, the study assessed the haemato-immunology, intestinal microbiome, and growth performance of the animals. For this, 30 juvenile Nile tilapia were used in the in vitro assay and 180 (60 + 120) in the in vivo assays. In the in vitro assay, we found evidence of adhesion of the probiotic bacteria to the intestinal mucus of fish, corroborated in the 15-day in vivo assay, in which the count of B. licheniformis was significantly higher in fish fed with probiotic when compared to fish of the control group. Furthermore, in the 50-day in vivo trial, a metagenomic analysis provided evidence for the modulation of the intestine microbiome of Nile tilapia by dietary supplementation of the probiotic. In addition, there was an increase in species richness, higher abundance of potentially probiotic autochthonous species and a lower abundance of Aeromonas sp. when the animals were fed the supplemented diet. Finally, no significant differences were observed in growth performance and haemato-immunological analyses, suggesting no harm to fish health when the product was supplemented for 15 and 50 days. The in vitro results indicate that the multi-strain probiotics were able to adhere to the intestinal mucus of Nile tilapia. Additionally, a modulation of the intestinal microbiome was evidenced in the in vivo assay.},
}
@article {pmid39117673,
year = {2024},
author = {An, L and Liu, X and Wang, J and Xu, J and Chen, X and Liu, X and Hu, B and Nie, Y and Wu, XL},
title = {Global diversity and ecological functions of viruses inhabiting oil reservoirs.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6789},
pmid = {39117673},
issn = {2041-1723},
support = {32130004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32161133023//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91951204//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170113//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Oil and Gas Fields/virology/microbiology ; *Viruses/genetics/classification/isolation &amp; purification ; *Metagenome/genetics ; *Biodiversity ; Microbiota/genetics ; Genome, Viral/genetics ; Phylogeny ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; },
abstract = {Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.},
}
@article {pmid39117653,
year = {2024},
author = {Wu, Z and Liu, T and Chen, Q and Chen, T and Hu, J and Sun, L and Wang, B and Li, W and Ni, J},
title = {Unveiling the unknown viral world in groundwater.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6788},
pmid = {39117653},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 423B2703//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Groundwater/microbiology/virology ; *Viruses/genetics/classification/isolation &amp; purification ; *Virome/genetics ; *Bacteria/genetics/virology/metabolism/classification ; *Metagenomics ; China ; Archaea/virology/genetics/metabolism ; Phylogeny ; Water Microbiology ; Metagenome ; Genome, Viral/genetics ; },
abstract = {Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species (≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.},
}
@article {pmid39116611,
year = {2024},
author = {Huang, X and Toro, M and Reyes-Jara, A and Moreno-Switt, AI and Adell, AD and Oliveira, CJB and Bonelli, RR and Gutiérrez, S and Álvarez, FP and Rocha, ADL and Kraychete, GB and Chen, Z and Grim, C and Brown, E and Bell, R and Meng, J},
title = {Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations.},
journal = {Water research},
volume = {264},
number = {},
pages = {122208},
doi = {10.1016/j.watres.2024.122208},
pmid = {39116611},
issn = {1879-2448},
abstract = {Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.},
}
@article {pmid39113128,
year = {2024},
author = {Robino, P and Galosi, L and Bellato, A and Vincenzetti, S and Gonella, E and Ferrocino, I and Serri, E and Biagini, L and Roncarati, A and Nebbia, P and Menzio, C and Rossi, G},
title = {Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome.},
journal = {Biological research},
volume = {57},
number = {1},
pages = {50},
pmid = {39113128},
issn = {0717-6287},
mesh = {Animals ; Bees/cytology/drug effects/enzymology/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects/physiology ; Hemocytes ; *Hemolymph/cytology ; Immunity, Innate ; Italy ; *Monophenol Monooxygenase/metabolism ; *Probiotics/administration &amp; dosage ; },
abstract = {BACKGROUND: In this study, a probiotic mixture (Honeybeeotic) consisting of seven bacterial strains isolated from a unique population of honeybees (Apis mellifera ligustica) was used. That honeybee population was located in the Roti Abbey locality of the Marche Region in Italy, an area isolated from human activities, and genetic contamination from other honeybee populations. The aim was to investigate the effects of this probiotic mixture on the innate immunity and intestinal microbiome of healthy common honeybees in two hives of the same apiary. Hive A received a diet of 50% glucose syrup, while hive B received the same syrup supplemented with the probiotics, both administered daily for 1 month. To determine whether the probiotic altered the immune response, phenoloxidase activity and hemolymph cellular subtype count were investigated. Additionally, metagenomic approaches were used to analyze the effects on gut microbiota composition and function, considering the critical role the gut microbiota plays in modulating host physiology.<br><br>RESULTS: The results revealed differences in hemocyte populations between the two hives, as hive A exhibited higher counts of oenocytoids and granulocytes. These findings indicated that the dietary supplementation with the probiotic mixture was safe and well-tolerated. Furthermore, phenoloxidase activity significantly decreased in hive B (1.75&#x2009;&#xb1;&#x2009;0.19 U/mg) compared to hive A (3.62&#x2009;&#xb1;&#x2009;0.44 U/mg, p&#x2009;<&#x2009;0.005), suggesting an improved state of well-being in the honeybees, as they did not require activation of immune defense mechanisms. Regarding the microbiome composition, the probiotic modulated the gut microbiota in hive B compared to the control, retaining core microbiota components while causing both positive and negative variations. Notably, several genes, particularly KEGG genes involved in amino acid metabolism, carbohydrate metabolism, and branched-chain amino acid (BCAA) transport, were more abundant in the probiotic-fed group, suggesting an effective nutritional supplement for the host.<br><br>CONCLUSIONS: This study advocated that feeding with this probiotic mixture induces beneficial immunological effects and promoted a balanced gut microbiota with enhanced metabolic activities related to digestion. The use of highly selected probiotics was shown to contribute to the overall well-being of the honeybees, improving their immune response and gut health.},
}
@article {pmid39113058,
year = {2024},
author = {Valdes, AM and Louca, P and Visconti, A and Asnicar, F and Bermingham, K and Nogal, A and Wong, K and Michelotti, GA and Wolf, J and Segata, N and Spector, TD and Berry, SE and Falchi, M and Menni, C},
title = {Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {321},
pmid = {39113058},
issn = {1741-7015},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Vitamin A/blood ; *Carotenoids/blood/metabolism ; Female ; Middle Aged ; Male ; *Retinoids/metabolism ; Aged ; Diet ; Feces/microbiology ; Adult ; },
abstract = {BACKGROUND: Vitamin A is essential for physiological processes like vision and immunity. Vitamin A's effect on gut microbiome composition, which affects absorption and metabolism of other vitamins, is still unknown. Here we examined the relationship between gut metagenome composition and six vitamin A-related metabolites (two retinoid: -retinol, 4 oxoretinoic acid (oxoRA) and four carotenoid metabolites, including beta-cryptoxanthin and three carotene diols).<br><br>METHODS: We included 1053 individuals from the TwinsUK cohort with vitamin A-related metabolites measured in serum and faeces, diet history, and gut microbiome composition assessed by shotgun metagenome sequencing. Results were replicated in 327 women from the ZOE PREDICT-1 study.<br><br>RESULTS: Five vitamin A-related serum metabolites were positively correlated with microbiome alpha diversity (r&#x2009;=&#x2009;0.15 to r&#x2009;=&#x2009;0.20, p&#x2009;<&#x2009;4&#x2009;&#xd7;&#x2009;10[-6]). Carotenoid compounds were positively correlated with the short-chain fatty-acid-producing bacteria Faecalibacterium prausnitzii and Coprococcus eutactus. Retinol was not associated with any microbial species. We found that gut microbiome composition could predict circulating levels of carotenoids and oxoretinoic acid with AUCs ranging from 0.66 to 0.74 using random forest models, but not retinol (AUC&#x2009;=&#x2009;0.52). The healthy eating index (HEI) was strongly associated with gut microbiome diversity and with all carotenoid compounds, but not retinoids. We investigated the mediating role of carotenoid compounds on the effect of a healthy diet (HEI) on gut microbiome diversity, finding that carotenoids significantly mediated between 18 and 25% of the effect of HEI on gut&#xa0;microbiome alpha diversity.<br><br>CONCLUSIONS: Our results show strong links between circulating carotene compounds and gut microbiome composition and potential links to a healthy diet pattern.},
}
@article {pmid39110709,
year = {2024},
author = {Lee, YM and Choi, KM and Mun, SH and Yoo, JW and Jung, JH},
title = {Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308246},
pmid = {39110709},
issn = {1932-6203},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Republic of Korea ; Animals ; *Isopoda/microbiology ; Water Pollutants, Chemical/toxicity/adverse effects ; Metagenomics/methods ; },
abstract = {Plastics pose a considerable challenge to aquatic ecosystems because of their increasing global usage and non-biodegradable properties. Coastal plastic debris can persist in ecosystems; however, its effects on resident organisms remain unclear. A metagenomic analysis of the isopoda Ligia, collected from clean (Nae-do, ND) and plastic-contaminated sites (Maemul-do, MD) in South Korea, was conducted to clarify the effects of microplastic contamination on the gut microbiota. Ligia gut microbiota's total operational taxonomic units were higher in ND than in MD. Alpha diversity did not differ significantly between the two Ligia gut microbial communities collected from ND and MD, although richness (Observed species) was lower in MD than in ND. Proteobacteria (67.47%, ND; 57.30%, MD) and Bacteroidetes (13.63%, ND; 20.76%, MD) were the most abundant phyla found at both sites. Significant different genera in Ligia from EPS-polluted sites were observed. Functional gene analysis revealed that 19 plastic degradation-related genes, including those encoding hydrogenase, esterase, and carboxylesterase, were present in the gut microbes of Ligia from MD, indicating the potential role of the Ligia gut microbiota in plastic degradation. This study provides the first comparative field evidence of the gut microbiota dynamics of plastic detritus consumers in marine ecosystems.},
}
@article {pmid39030686,
year = {2024},
author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB},
title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae132},
pmid = {39030686},
issn = {1751-7370},
support = {UM PRA 2022-2547//University of Miami Provost Research Award/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Holmes Fellowship/ ; //Kushlan Graduate Research Support Award/ ; 2023349872//NSF Graduate Research Fellowship Program/ ; //University of Miami Dean's Fellowship/ ; PG015171//Maytag Fellowship/ ; 80NSSC23K0676//National Aeronautics and Space Administration Exobiology Program/ ; },
mesh = {*Bacteriophages/genetics/isolation &amp; purification/classification ; *Anthozoa/virology/microbiology ; *Genome, Viral ; Animals ; *Bacteria/virology/genetics/classification ; Metagenome ; Symbiosis ; Coral Reefs ; Virome/genetics ; Prophages/genetics ; },
abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.},
}
@article {pmid39023219,
year = {2024},
author = {López-Beltrán, A and Botelho, J and Iranzo, J},
title = {Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae134},
pmid = {39023219},
issn = {1751-7370},
support = {PRE2020-092935//Agencia Estatal de Investigaci&#xf3;n of Spain/ ; UP2021-035//Spanish Ministry of Universities/ ; CEX2020-000999-S//Severo Ochoa Program for Centres of Excellence in R&amp;D of the Agencia Estatal de Investigaci&#xf3;n of Spain/ ; RYC-2017-22524//Ram&#xf3;n y Cajal Programme of the Spanish Ministry of Science/ ; PID2019-106618GA-I00//Agencia Estatal de Investigaci&#xf3;n of Spain/ ; SEV-2016-0672//Severo Ochoa Programme for Centres of Excellence in R&amp;D of the Agencia Estatal de Investigaci&#xf3;n of Spain/ ; //Comunidad de Madrid/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/classification/virology ; Metagenomics ; Plasmids/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Host Microbial Interactions ; Prophages/genetics/physiology ; },
abstract = {Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.},
}
@article {pmid39002480,
year = {2024},
author = {Singh, DP and Kumar, A and Prajapati, J and Bijalwan, V and Kumar, J and Amin, P and Kandoriya, D and Vidhani, H and Patil, GP and Bishnoi, M and Rawal, R and Das, S},
title = {Sexual dimorphism in neurobehavioural phenotype and gut microbial composition upon long-term exposure to structural analogues of bisphenol-A.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135178},
doi = {10.1016/j.jhazmat.2024.135178},
pmid = {39002480},
issn = {1873-3336},
mesh = {Animals ; *Phenols/toxicity ; Male ; *Gastrointestinal Microbiome/drug effects ; Female ; *Benzhydryl Compounds/toxicity ; *Sex Characteristics ; *Sulfones/toxicity ; *Endocrine Disruptors/toxicity ; *Behavior, Animal/drug effects ; Cytokines/metabolism ; Phenotype ; Mice ; Mice, Inbred C57BL ; Anxiety/chemically induced ; Depression/chemically induced ; Hippocampus/drug effects/metabolism ; Neurotransmitter Agents/metabolism ; Brain/drug effects/metabolism ; },
abstract = {Bisphenol S (BPS) and Bisphenol F (BPF), the analogues of the legacy endocrine disrupting chemical, Bisphenol A (BPA) are ubiquitous in the environment and present in various consumer goods, and potentially neurotoxic. Here, we studied sex-specific responses of bisphenols on behavioural phenotypes, including their association with pro-inflammatory biomarkers and altered neurotransmitters levels, and the key gut microbial abundances. Neurobehavioural changes, using standard test battery, biochemical and molecular estimations for inflammatory cytokines, neurotransmitters, and oxido-nitrosative stress markers, gene expression analysis using qRT-PCR, H&amp;E based histological investigations, gut permeability assays and Oxford Nanopore-based 16S-rRNA metagenomics sequencing for the gut microbial abundance estimations were performed. Bisphenol(s) exposure induces anxiety and depression-like behaviours, particularly in the male mice, with heightened pro-inflammatory cytokines levels and systemic endotoxemia, altered monoamine neurotransmitters levels/turnovers and hippocampal neuronal degeneration and inflammatory responses in the brain. They also increased gut permeability and altered microbial diversity, particularly in males. Present study provides evidence for sex-specific discrepancies in neurobehavioural phenotypes and gut microbiota, which necessitate a nuanced understanding of sex-dependent responses to bisphenols. The study contributes to ongoing discussions on the multifaceted implications of bisphenols exposure and underscores the need for tailored regulatory measures to mitigate potential health risks associated with them.},
}
@article {pmid38986408,
year = {2024},
author = {Xie, ST and Zhu, D and Song, YQ and Zhu, YG and Ding, LJ},
title = {Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135133},
doi = {10.1016/j.jhazmat.2024.135133},
pmid = {38986408},
issn = {1873-3336},
mesh = {*Oligochaeta/microbiology ; Animals ; *Virulence Factors/genetics ; *Soil Microbiology ; *Ecosystem ; Microbiota ; Bacteria/genetics/metabolism/pathogenicity ; },
abstract = {Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.},
}
@article {pmid38986403,
year = {2024},
author = {Jiang, Y and Zhou, C and Khan, A and Zhang, X and Mamtimin, T and Fan, J and Hou, X and Liu, P and Han, H and Li, X},
title = {Environmental risks of mask wastes binding pollutants: Phytotoxicity, microbial community, nitrogen and carbon cycles.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135058},
doi = {10.1016/j.jhazmat.2024.135058},
pmid = {38986403},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Nitrogen ; Carbon Cycle ; Microbiota/drug effects ; Bacteria/drug effects/genetics/metabolism ; Medicago sativa/drug effects ; },
abstract = {The increasing contamination of mask wastes presents a significant global challenge to ecological health. However, there is a lack of comprehensive understanding regarding the environmental risks that mask wastes pose to soil. In this study, a total of 12 mask wastes were collected from landfills. Mask wastes exhibited negligible morphological changes, and bound eight metals and four types of organic pollutants. Masks combined with pollutants inhibited the growth of alfalfa and Elymus nutans, reducing underground biomass by 84.6 %. Mask wastes decreased the Chao1 index and the relative abundances (RAs) of functional bacteria (Micrococcales, Gemmatimonadales, and Sphingomonadales). Metagenomic analysis showed that mask wastes diminished the RAs of functional genes associated with nitrification (amoABC and HAO), denitrification (nirKS and nosZ), glycolysis (gap2), and TCA cycle (aclAB and mdh), thereby inhibiting the nitrogen transformation and ATP production. Furthermore, some pathogenic viruses (Herpesviridae and Tunggulvirus) were also found on the mask wastes. Structural equation models demonstrated that mask wastes restrained soil enzyme activities, ultimately affecting nitrogen and carbon cycles. Collectively, these evidences indicate that mask wastes contribute to soil health and metabolic function disturbances. This study offers a new perspective on the potential environmental risks associated with the improper disposal of masks.},
}
@article {pmid38981230,
year = {2024},
author = {Tang, X and Chen, Y and Zheng, W and Chen, L and Liu, H and Li, M and Yang, Y},
title = {Enhancing neonicotinoid removal in recirculating constructed wetlands: The impact of Fe/Mn biochar and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135139},
doi = {10.1016/j.jhazmat.2024.135139},
pmid = {38981230},
issn = {1873-3336},
mesh = {*Wetlands ; *Charcoal/chemistry ; *Water Pollutants, Chemical/metabolism ; *Neonicotinoids/chemistry/metabolism ; *Biodegradation, Environmental ; *Iron/chemistry ; Manganese ; Wastewater/chemistry ; Nitrogen/metabolism ; Microbiota ; Phosphorus/chemistry ; Bacteria/genetics/metabolism ; Adsorption ; Insecticides/metabolism ; Waste Disposal, Fluid/methods ; Nitro Compounds ; },
abstract = {Neonicotinoids pose significant environmental risks due to their widespread use, persistence, and challenges in elimination. This study explores the effectiveness of Fe/Mn biochar in enhancing the removal efficiency of neonicotinoids in recirculating constructed wetlands (RCWs). Results demonstrated that incorporating Fe/Mn biochar into RCWs significantly improved the removal of COD, NH4[+]-N, TN, TP, imidacloprid (IMI), and acetamiprid (ACE). However, the simultaneous presence of IMI and ACE in the RCWs hindered the elimination of NH4[+]-N, TN, and TP from wastewater. The enhanced removal of nutrients and pollutants by Fe/Mn biochar was attributed to its promotion of carbon, nitrogen, and phosphorus cycling in RCWs, along with its facilitation of the adsorption and biodegradation of IMI and ACE. Metagenomics analysis demonstrated that Fe/Mn biochar altered the structure and diversity of microbial communities in RCWs. A total of 17 biodegradation genes (BDGs) and two pesticide degradation genes (PDGs) were identified within RCWs, with Fe/Mn biochar significantly increasing the abundance of BDGs such as cytochrome P450. The potential host genera for these BDGs/PDGs were identified as Betaproteobacteria, Acidobacteria, Nitrospiraceae, Gemmatimonadetes, and Bacillus. This study offers valuable insights into how Fe/Mn biochar enhances pesticide removal and its potential application in constructed wetland systems for treating pesticide-contaminated wastewater.},
}
@article {pmid38980017,
year = {2024},
author = {Haghani, NB and Lampe, RH and Samuel, BS and Chalasani, SH and Matty, MA},
title = {Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0016924},
pmid = {38980017},
issn = {2165-0497},
support = {80NSSC22K0250//National Aeronautics and Space Administration (NASA)/ ; P40 OD010440/OD/NIH HHS/United States ; DP2DK116645//HHS | National Institutes of Health (NIH)/ ; R01 MH096881/MH/NIMH NIH HHS/United States ; R01MH096881//HHS | National Institutes of Health (NIH)/ ; CSP-503338//U.S. Department of Energy (DOE)/ ; DP2 DK116645/DK/NIDDK NIH HHS/United States ; 2011023//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Caenorhabditis elegans/microbiology ; *Microbiota/genetics ; *Skin/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; },
abstract = {UNLABELLED: In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple "skin microbiome." We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal's gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts.<br><br>IMPORTANCE: The genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.},
}
@article {pmid38972205,
year = {2024},
author = {Jachimowicz, P and Mądzielewska, W and Cydzik-Kwiatkowska, A},
title = {Microplastics in granular sequencing batch reactors: Effects on pollutant removal dynamics and the microbial community.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135061},
doi = {10.1016/j.jhazmat.2024.135061},
pmid = {38972205},
issn = {1873-3336},
mesh = {*Bioreactors ; *Water Pollutants, Chemical/metabolism ; *Microplastics/toxicity ; *Phosphorus/metabolism/chemistry ; *Nitrogen/metabolism ; Sewage/microbiology ; Polyethylene Terephthalates/metabolism/chemistry ; Polyethylene/metabolism/chemistry ; Microbiota ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; },
abstract = {This study investigated the relationship between microplastic (MP) presence and pollutant removal in granular sludge sequencing batch reactors (GSBRs). Two types of MPs, polyethylene (PE) and polyethylene terephthalate (PET), were introduced in varying concentrations to assess their effects on microbial community dynamics and rates of nitrogen, phosphorus, and organic compound removal. The study revealed type-dependent variations in the deposition of MPs within the biomass, with PET-MPs exhibiting a stronger affinity for accumulation in biomass. A 50 mg/L dose of PET-MP decreased COD removal efficiency by approximately 4 % while increasing P-PO4 removal efficiency by around 7 % compared to the control reactor. The rate of nitrogen compounds removal decreased with higher PET-MP dosages but increased with higher PE-MP dosages. An analysis of microbial activity and gene abundance highlighted the influence of MPs on the expression of the nosZ and ppk1 genes, which code enzymes responsible for nitrogen and phosphorus transformations. The study also explored shifts in microbial community structure, revealing alterations with changes in MP dose and type. This research contributes valuable insights into the complex interactions between MP, microbial communities, and pollutant removal processes in GSBR systems, with implications for the sustainable management of wastewater treatment in the presence of MP.},
}
@article {pmid38954855,
year = {2024},
author = {Nie, C and Chen, L and Zhao, B and Wu, Z and Zhang, M and Yan, Y and Li, B and Xia, Y},
title = {Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135074},
doi = {10.1016/j.jhazmat.2024.135074},
pmid = {38954855},
issn = {1873-3336},
mesh = {*Sulfamethoxazole/metabolism ; Microbial Consortia ; Adaptation, Physiological ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Ammonia/metabolism ; Anti-Bacterial Agents/metabolism ; Drug Resistance, Microbial/genetics ; Anaerobiosis ; },
abstract = {Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.},
}
@article {pmid38943887,
year = {2024},
author = {Zhou, Y and Wang, Y and Yao, S and Zhao, X and Kong, Q and Cui, L and Zhang, H},
title = {Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135060},
doi = {10.1016/j.jhazmat.2024.135060},
pmid = {38943887},
issn = {1873-3336},
mesh = {*Biodegradation, Environmental ; *Petroleum Pollution ; *Microbiota ; *Petroleum/metabolism ; *Seawater/microbiology ; *Water Pollutants, Chemical/metabolism ; *Hydrocarbons/metabolism ; Bacteria/metabolism/genetics/classification ; Oceans and Seas ; Adaptation, Physiological ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.},
}
@article {pmid38916350,
year = {2024},
author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G},
title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0266223},
pmid = {38916350},
issn = {2165-0497},
support = {20/2022-ECR-II//Indian Council of Medical Research (ICMR)/ ; },
mesh = {Animals ; *Microbiota/genetics/drug effects ; *Neanderthals/genetics/microbiology ; *DNA, Ancient/analysis ; *Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Feces/microbiology ; Metagenome ; Drug Resistance, Microbial/genetics ; Europe ; Fossils/microbiology ; },
abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.<br><br>IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.},
}
@article {pmid38916335,
year = {2024},
author = {Yin, X-F and Ye, T and Chen, H-L and Liu, J and Mu, X-F and Li, H and Wang, J and Hu, Y-J and Cao, H and Kang, W-Q},
title = {The microbiome compositional and functional differences between rectal mucosa and feces.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0354923},
pmid = {38916335},
issn = {2165-0497},
support = {2020001//Shenzhen Nanshan District Scientific Research program of the People's Republic of China/ ; 006/2023/SKL//The Science and Tchnology Development Fund, Macau SAR/ ; },
mesh = {Humans ; *Feces/microbiology ; Male ; *Intestinal Mucosa/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Rectum/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; Colonic Polyps/microbiology ; Metagenomics ; Colorectal Neoplasms/microbiology ; },
abstract = {UNLABELLED: In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.<br><br>IMPORTANCE: This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.},
}
@article {pmid38916334,
year = {2024},
author = {Du, L and Wang, J and Qiu, X and Wang, Q and Peng, H and Huang, J and Yang, F and Liu, Z and Qi, R},
title = {Clostridium sporogenes increases fat accumulation in mice by enhancing energy absorption and adipogenesis.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0411623},
pmid = {38916334},
issn = {2165-0497},
support = {U21A20245, 32272830//MOST | National Natural Science Foundation of China (NSFC)/ ; 23509J//Financial Resourced Program of Chongqing/ ; },
mesh = {Animals ; Mice ; *Adipogenesis ; *Energy Metabolism ; *Gastrointestinal Microbiome/physiology ; *Clostridium/metabolism/genetics ; Male ; Adipose Tissue/metabolism ; Mice, Inbred C57BL ; Liver/metabolism ; Lipid Metabolism ; Triglycerides/metabolism ; },
abstract = {UNLABELLED: Gut bacteria belonging to the Clostridium family play a pivotal role in regulating host energy balance and metabolic homeostasis. As a commensal bacterium, Clostridium sporogenes has been implicated in modulating host energy homeostasis, albeit the underlying mechanism remains elusive. Therefore, this study aimed to investigate the impact of C. sporogenes supplementation on various physiological parameters, intestinal morphology, particularly adipose tissue accumulation, and glucolipid metabolism in mice. The findings reveal that mice supplemented with C. sporogenes for 6 weeks exhibited a notable increase in body weight, fat mass, adipocyte size, and serum triglyceride (TG) levels. Notably, the increased fat accumulation is observed despite consistent feed intake in treated mice. Mechanistically, C. sporogenes supplementation significantly improved the structure integrity of intestinal villi and enhanced energy absorption efficiency while reducing excretion of carbohydrates and fatty acids in feces. This was accompanied by upregulation of glucose and fatty acid transporter expression. Furthermore, supplementation with C. sporogenes promoted adipogenesis in both liver and adipose tissues, as evidenced by increased levels of hepatic pyruvate, acetyl-CoA, and TG, along with elevated expression levels of genes associated with lipid synthesis. Regarding the microbiological aspect, C. sporogenes supplementation correlated with an increased abundance of Clostridium genus bacteria and enhanced carbohydrate enzyme activity. In summary, C. sporogenes supplementation significantly promotes fat accumulation in mice by augmenting energy absorption and adipogenesis, possibly mediated by the expansion of Clostridium bacteria population with robust glycolipid metabolic ability.<br><br>IMPORTANCE: The Clostridia clusters have been implicated in energy metabolism, the specific species and underlying mechanisms remain unclear. This present study is the first to report Clostridium sporogenes is able to affect fat accumulation and glycolipid metabolism. We indicated that gavage of C. sporogenes promoted the adipogenesis and fat accumulation in mice by not only increasing the abundance of Clostridium bacteria but by also enhancing the metabolic absorption of carbohydrates and fatty acids significantly. Obviously, changes of gut microbiota caused by the C. sporogenes, especially the significant increase of Clostridium bacteria, contributed to the fat accumulation of mice. In addition, the enhancement of Clostridium genus bacteria remarkably improved the synthesis of hepatic pyruvate, acetyl-CoA, and triglyceride levels, as well as reduced the excretion of fecal carbohydrates, short-chain fatty acids, and free fatty acids remarkably. These findings will help us to understand the relationship of specific bacteria and host energy homeostasis.},
}
@article {pmid38916313,
year = {2024},
author = {Maqsood, R and Wu, LI and Brennan, DC and Lim, ES},
title = {Longitudinal alterations in the urinary virome of kidney transplant recipients are influenced by BK viremia and patient sex.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0405523},
pmid = {38916313},
issn = {2165-0497},
support = {R00 DK107923/DK/NIDDK NIH HHS/United States ; R00DK107923//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *BK Virus/isolation &amp; purification/genetics ; Male ; Female ; *Polyomavirus Infections/urine/virology ; *Virome ; *Viremia/urine ; Middle Aged ; Adult ; *Transplant Recipients ; Longitudinal Studies ; Tumor Virus Infections/urine/virology ; Aged ; Sex Factors ; Urine/virology ; },
abstract = {UNLABELLED: Little is known about the urinary virome and how it interacts with the host, particularly in renal transplant diseases. Using metagenomic sequencing, we characterized the urinary virome of 23 kidney transplant recipients longitudinally (11 BKV+ patients and 12 BKV- patients). We applied linear mixed effects models, PERMANOVA, k-means clustering, and MaAsLin2 algorithms to determine virome signatures associated with post-transplant time, BK viremia status, and patient sex. We found that the richness and alpha diversity of urinary virome were significantly different in renal transplant recipients with BKV+ over time in comparison to BKV- (richness P = 0.012, alpha P < 0.0001). Female BKV- patients had significantly higher virome richness than males (P = 0.0063). Virome beta diversity was significantly different between patients by BKV status (P < 0.001). Additionally, we identified underlying interactions between patient sex and BKV status, in terms of virome beta diversity (P = 0.008). BK polyomavirus infections were primarily of subtypes IA, IB1, and IB2. The non-BK dominant samples clustered into six urinary virome community states. BKV- samples had more anelloviruses than BKV+ samples though this difference was not statistically significant. Lastly, we identified specific viruses, associated with BKV+ and time in our samples. Our results indicate that dynamic alterations in the urinary virome over the post-transplant period in kidney transplant recipients can be shaped by BK viremia and patient sex. These findings advance our fundamental understanding of the urinary virome and support a new line of investigation in renal disease and transplantation.<br><br>IMPORTANCE: The urinary microbiome is increasingly implicated in renal health and disease. While most research focuses on bacteria communities of the microbiome, factors that influence the urinary virome are not understood. Here, we investigated the urinary virome of 23 adult kidney transplant recipients longitudinally over 14 weeks post-transplant. We show that alterations in the urinary virome are associated with kidney transplant recipients with BK polyomavirus viremia that can lead to BK nephropathy and allograft rejection. By modeling the temporal dynamics post-transplant, we delineated specific profiles of the urinary virome associated with patient sex and urinary community states. These findings reveal fundamental aspects of the urinary virome that can be leveraged to better manage kidney diseases.},
}
@article {pmid38908447,
year = {2024},
author = {Gao, H and Guo, Z and He, X and Yang, J and Jiang, L and Yang, A and Xiao, X and Xu, R},
title = {Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142680},
doi = {10.1016/j.chemosphere.2024.142680},
pmid = {38908447},
issn = {1879-1298},
mesh = {*Oryza/microbiology ; *Metals, Heavy/metabolism ; *Plant Leaves/metabolism ; *Microbiota/drug effects ; Stress, Physiological ; Air Pollutants/toxicity ; Pantoea/physiology ; },
abstract = {Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.},
}
@article {pmid38904365,
year = {2024},
author = {Dandachi, I and Alrezaihi, A and Amin, D and AlRagi, N and Alhatlani, B and Binjomah, A and Aleisa, K and Dong, X and Hiscox, JA and Aljabr, W},
title = {Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0066524},
pmid = {38904365},
issn = {2165-0497},
support = {019-034//King Fahad Medical City (KFMC)/ ; },
mesh = {Humans ; Saudi Arabia/epidemiology ; *Influenza, Human/virology/epidemiology/microbiology ; *Phylogeny ; Male ; *Nasopharynx/virology/microbiology ; *Whole Genome Sequencing ; Female ; Adult ; *Metagenomics ; Middle Aged ; *Influenza A virus/genetics/classification/isolation &amp; purification ; *Genome, Viral/genetics ; Adolescent ; Aged ; Young Adult ; Child ; Child, Preschool ; Molecular Epidemiology ; Infant ; Microbiota/genetics ; Antiviral Agents/pharmacology/therapeutic use ; },
abstract = {Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.},
}
@article {pmid38885765,
year = {2024},
author = {Di Gregorio, S and Niccolini, L and Seggiani, M and Strangis, G and Barbani, N and Vitiello, V and Becarelli, S and Petroni, G and Yan, X and Buttino, I},
title = {Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate).},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142603},
doi = {10.1016/j.chemosphere.2024.142603},
pmid = {38885765},
issn = {1879-1298},
mesh = {Animals ; *Copepoda ; *Biodegradation, Environmental ; *Microbiota ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Polyesters/metabolism ; Adipates/metabolism ; Polymers/metabolism ; RNA, Ribosomal, 16S/genetics ; Plankton/metabolism ; Butylene Glycols ; },
abstract = {The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.},
}
@article {pmid38876324,
year = {2024},
author = {Wen, M and Zhang, Q and Li, Y and Cui, Y and Shao, J and Liu, Y},
title = {Influence of dissolved organic matter on the anaerobic biotransformation of roxarsone accompanying microbial community response.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142606},
doi = {10.1016/j.chemosphere.2024.142606},
pmid = {38876324},
issn = {1879-1298},
mesh = {*Biotransformation ; *Roxarsone/metabolism ; Anaerobiosis ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics/classification ; },
abstract = {Roxarsone (ROX), commonly employed as a livestock feed additive, largely remains unmetabolized and is subsequently excreted via feces. ROX could cause serious environmental risks due to its rapid transformation and high mobility in the anaerobic subsurface environment. Dissolved organic matter (DOM) is an important constituent of fecal organics in livestock waste and could affect the ROX biotransformation. Nonetheless, the underlying mechanisms governing the interaction between DOM and ROX biotransformation have not yet been elucidated in the anaerobic environment. In this study, the changes of ROX, metabolites, and microbial biomass in the solutions with varying DOM concentrations (0, 50, 100, 200, and 400 mg/L) under anaerobic environments were investigated during the ROX (200 mg/L) degradation. EEM-PARAFAC and metagenomic sequencing were combined to identify the dynamic shifts of DOM components and the functional microbial populations responsible for ROX degradation. Results indicated that DOM facilitated the anaerobic biotransformation of ROX and 200 mg/L ROX could be degraded completely in 28 h. The tryptophan-like within DOM functioned as a carbon source to promote the growth of microorganisms, thus accelerating the degradation of ROX. The mixed microflora involved in ROX anaerobic degrading contained genes associated with arsenic metabolism (arsR, arsC, acr3, arsA, nfnB, and arsB), and arsR, arsC, acr3 exhibited high microbial diversity. Variations in DOM concentrations significantly impacted the population dynamics of microorganisms involved in arsenic metabolism (Proteiniclasticum, Exiguobacterium, Clostridium, Proteiniphilum, Alkaliphilus, and Corynebacterium spp.), which in turn affected the transformation of ROX and its derivatives. This study reveals the mechanism of ROX degradation influenced by the varying concentrations of DOM under anaerobic environments, which is important for the prevention of arsenic contamination with elevated levels of organic matter.},
}
@article {pmid38599786,
year = {2024},
author = {Su, ACY and Ding, X and Lau, HCH and Kang, X and Li, Q and Wang, X and Liu, Y and Jiang, L and Lu, Y and Liu, W and Ding, Y and Cheung, AH and To, KF and Yu, J},
title = {Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase.},
journal = {Gut},
volume = {73},
number = {9},
pages = {1478-1488},
doi = {10.1136/gutjnl-2023-330835},
pmid = {38599786},
issn = {1468-3288},
mesh = {Animals ; *Colorectal Neoplasms/microbiology/pathology/prevention &amp; control ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; *Probiotics/therapeutic use ; *Lactococcus lactis ; *Feces/microbiology ; *alpha-Mannosidase/metabolism ; *Carcinogenesis ; Mice, Transgenic ; Female ; Male ; },
abstract = {OBJECTIVE: Probiotic Lactococcus lactis is known to confer health benefits to humans. Here, we aimed to investigate the role of L. lactis in colorectal cancer (CRC).<br><br>DESIGN: L. lactis abundance was evaluated in patients with CRC (n=489) and healthy individuals (n=536). L. lactis was isolated from healthy human stools with verification by whole genome sequencing. The effect of L. lactis on CRC tumourigenesis was assessed in transgenic Apc [Min/+] mice and carcinogen-induced CRC mice. Faecal microbiota was profiled by metagenomic sequencing. Candidate proteins were characterised by nano liquid chromatography-mass spectrometry. Biological function of L. lactis conditioned medium (HkyuLL 10-CM) and functional protein was studied in human CRC cells, patient-derived organoids and xenograft mice.<br><br>RESULTS: Faecal L. lactis was depleted in patients with CRC. A new L. lactis strain was isolated from human stools and nomenclated as HkyuLL 10. HkyuLL 10 supplementation suppressed CRC tumourigenesis in Apc [Min/+] mice, and this tumour-suppressing effect was confirmed in mice with carcinogen-induced CRC. Microbiota profiling revealed probiotic enrichment including Lactobacillus johnsonii in HkyuLL 10-treated mice. HkyuLL 10-CM significantly abrogated the growth of human CRC cells and patient-derived organoids. Such protective effect was attributed to HkyuLL 10-secreted proteins, and we identified that &#x3b1;-mannosidase was the functional protein. The antitumourigenic effect of &#x3b1;-mannosidase was demonstrated in human CRC cells and organoids, and its supplementation significantly reduced tumour growth in xenograft mice.<br><br>CONCLUSION: HkyuLL 10 suppresses CRC tumourigenesis in mice through restoring gut microbiota and secreting functional protein &#x3b1;-mannosidase. HkyuLL 10 administration may serve as a prophylactic measure against CRC.},
}
@article {pmid39109810,
year = {2024},
author = {Tomar, SS and Khairnar, K},
title = {Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation.},
journal = {Journal of medical virology},
volume = {96},
number = {8},
pages = {e29829},
doi = {10.1002/jmv.29829},
pmid = {39109810},
issn = {1096-9071},
support = {//National Environmental Engineering Research Institute/ ; //Council of Scientific and Industrial Research, India/ ; //CSIR-NEERI/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Lumpy skin disease virus/isolation &amp; purification/genetics/classification ; Oropharynx/virology/microbiology ; Animals ; India ; Genome, Viral/genetics ; Nasopharynx/virology/microbiology ; Respiratory System/microbiology/virology ; Male ; Whole Genome Sequencing ; SARS-CoV-2/genetics/isolation &amp; purification/classification ; Female ; Adult ; COVID-19/diagnosis/virology ; Lumpy Skin Disease/virology ; },
abstract = {Lumpy skin disease virus (LSDV), a double-stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS-CoV-2 surveillance underwent whole-genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.},
}
@article {pmid39104524,
year = {2024},
author = {Han, L and Liu, X and Lan, Y and Hua, Y and Fan, Z and Li, Y},
title = {Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1416185},
pmid = {39104524},
issn = {1664-3224},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenomics/methods ; Female ; Child, Preschool ; Infant ; *Feces/microbiology ; Immunoglobulins, Intravenous/therapeutic use ; Metagenome ; Child ; Bacteria/classification/genetics/isolation &amp; purification ; Case-Control Studies ; },
abstract = {BACKGROUND: Kawasaki disease (KD) has been considered as the most common required pediatric cardiovascular diseases among the world. However, the molecular mechanisms of KD were not fully underlined, leading to a confused situation in disease management and providing precious prognosis prediction. The disorders of gut microbiome had been identified among several cardiovascular diseases and inflammation conditions. Therefore, it is urgent to elucidate the characteristics of gut microbiome in KD and demonstrate its potential role in regulating intravenous immunoglobulin (IVIG) resistance and coronary artery injuries.<br><br>METHODS: A total of 96 KD children and 62 controls were enrolled in the study. One hundred forty fecal samples had been harvested from KD patients, including individuals before or after IVIG treatment, with or without early coronary artery lesions and IVIG resistance. Fecal samples had been collected before and after IVIG administration and stored at -80&#xb0;C. Then, metagenomic analysis had been done using Illumina NovaSeq 6000 platform. After that, the different strains and functional differences among comparisons were identified.<br><br>RESULTS: First, significant changes had been observed between KD and their controls. We found that the decrease of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides uniformis, and Bacteroides ovatus and the increase of pathogenic bacteria Finegoldia magna, Abiotrophia defectiva, and Anaerococcus prevotii perhaps closely related to the incidence of KD. Then, metagenomic and responding functional analysis demonstrated that short-chain fatty acid pathways and related strains were associated with different outcomes of therapeutic efficacies. Among them, the reduction of Bacteroides thetaiotaomicron, the enrichment of Enterococcus faecalis and antibiotic resistance genes had been found to be involved in IVIG resistance of KD. Moreover, our data also revealed several potential pathogenetic microbiome of that KD patients with coronary artery lesions.<br><br>CONCLUSION: These results strongly proved that distinct changes in the gut microbiome of KD and the dysfunction of gut microbiomes should be responsible for the pathogenesis of KD and significantly impact the prognosis of KD.},
}
@article {pmid38977908,
year = {2024},
author = {Crocker, K and Lee, KK and Chakraverti-Wuerthwein, M and Li, Z and Tikhonov, M and Mani, M and Gowda, K and Kuehn, S},
title = {Environmentally dependent interactions shape patterns in gene content across natural microbiomes.},
journal = {Nature microbiology},
volume = {9},
number = {8},
pages = {2022-2037},
pmid = {38977908},
issn = {2058-5276},
support = {EF 2025293//National Science Foundation (NSF)/ ; DGE 174604//National Science Foundation (NSF)/ ; EF 2025521//National Science Foundation (NSF)/ ; R01GM151538//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 220020499//James S. McDonnell Foundation (McDonnell Foundation)/ ; },
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Denitrification ; Metagenomics ; Genotype ; Soil/chemistry ; },
abstract = {Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.},
}
@article {pmid38907008,
year = {2024},
author = {Huang, L and Guo, R and Li, S and Wu, X and Zhang, Y and Guo, S and Lv, Y and Xiao, Z and Kang, J and Meng, J and Zhou, P and Ma, J and You, W and Zhang, Y and Yu, H and Zhao, J and Huang, G and Duan, Z and Yan, Q and Sun, W},
title = {A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome.},
journal = {Nature microbiology},
volume = {9},
number = {8},
pages = {2185-2200},
pmid = {38907008},
issn = {2058-5276},
mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; Fungi/genetics/classification/isolation &amp; purification ; Phylogeny ; Genome, Microbial ; Metagenome ; Viruses/genetics/classification/isolation &amp; purification ; Vaginosis, Bacterial/microbiology ; },
abstract = {The human vagina harbours diverse microorganisms-bacteria, viruses and fungi-with profound implications for women's health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data and fungal cultivation to establish the Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 fungal species and 4,263 viral operational taxonomic units. Notably, over 25% of prokaryotic species and 85% of viral operational taxonomic units remain uncultured. This collection significantly enriches genomic diversity, especially for prevalent vaginal pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) and Amygdalobacter spp. (BVAB2 and related species). Leveraging VMGC, we characterize functional traits of prokaryotes, notably Saccharofermentanales (an underexplored yet prevalent order), along with prokaryotic and eukaryotic viruses, offering insights into their niche adaptation and potential roles in the vagina. VMGC serves as a valuable resource for studying vaginal microbiota and its impact on vaginal health.},
}
@article {pmid38900914,
year = {2024},
author = {Heinz, JM and Lu, J and Huebner, LK and Salzberg, SL and Sommer, M and Rosales, SM},
title = {Novel metagenomics analysis of stony coral tissue loss disease.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {8},
pages = {},
doi = {10.1093/g3journal/jkae137},
pmid = {38900914},
issn = {2160-1836},
support = {R35-GM130151/GF/NIH HHS/United States ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Metagenomics/methods ; Metagenome ; Computational Biology/methods ; Microbiota/genetics ; Coral Reefs ; },
abstract = {Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.},
}
@article {pmid38613058,
year = {2024},
author = {Lombardi, M and Troisi, J and Motta, BM and Torre, P and Masarone, M and Persico, M},
title = {Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613058},
issn = {2072-6643},
mesh = {Humans ; *Hypertension, Portal/metabolism/physiopathology/etiology ; *Gastrointestinal Microbiome/physiology ; *Liver/metabolism ; *Dysbiosis ; Bacterial Translocation ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.},
}
@article {pmid38600293,
year = {2024},
author = {Jiang, MZ and Liu, C and Xu, C and Jiang, H and Wang, Y and Liu, SJ},
title = {Gut microbial interactions based on network construction and bacterial pairwise cultivation.},
journal = {Science China. Life sciences},
volume = {67},
number = {8},
pages = {1751-1762},
pmid = {38600293},
issn = {1869-1889},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteria/genetics/classification/metabolism ; *Feces/microbiology ; *Coculture Techniques ; Metagenome ; Microbial Interactions ; Metagenomics/methods ; },
abstract = {Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.},
}
@article {pmid38594499,
year = {2024},
author = {Franceschetti, L and Lodetti, G and Blandino, A and Amadasi, A and Bugelli, V},
title = {Exploring the role of the human microbiome in forensic identification: opportunities and challenges.},
journal = {International journal of legal medicine},
volume = {138},
number = {5},
pages = {1891-1905},
pmid = {38594499},
issn = {1437-1596},
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; DNA Fingerprinting ; Metagenomics/methods ; },
abstract = {Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.},
}
@article {pmid39103408,
year = {2024},
author = {Atencio, B and Geisler, E and Rubin-Blum, M and Bar-Zeev, E and Adar, EM and Ram, R and Ronen, Z},
title = {Metabolic adaptations underpin high productivity rates in relict subsurface water.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18126},
pmid = {39103408},
issn = {2045-2322},
support = {1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1359/23//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 1068/20//Israel Science Foundation/ ; 221-17-002//Ministry of Energy, Israel/ ; },
mesh = {*Groundwater/microbiology ; Israel ; Bacteria/metabolism/genetics/classification ; Adaptation, Physiological ; Water Microbiology ; Microbiota ; },
abstract = {Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel's Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L[-1] d[-1] (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.},
}
@article {pmid39091768,
year = {2024},
author = {Quezada-Romegialli, C and Quiroga-Carmona, M and D'Elía, G and Harrod, C and Storz, JF},
title = {Diet of Andean leaf-eared mice (Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39091768},
issn = {2692-8205},
support = {R01 HL159061/HL/NHLBI NIH HHS/United States ; },
abstract = {On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ('aolian deposits'). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such plants may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.},
}
@article {pmid38976951,
year = {2024},
author = {Islam, W and Zeng, F and Almoallim, HS and Ansari, MJ},
title = {Unveiling soil animal community dynamics beneath dominant shrub species in natural desert environment: Implications for ecosystem management and conservation.},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121697},
doi = {10.1016/j.jenvman.2024.121697},
pmid = {38976951},
issn = {1095-8630},
mesh = {*Soil ; *Ecosystem ; *Desert Climate ; Animals ; Conservation of Natural Resources ; Biodiversity ; },
abstract = {The Taklimakan Desert, known for extreme aridity and unique ecological challenges, maintains a delicate life balance beneath its harsh surface. This study investigates intricate dynamics of soil animal communities within this desert ecosystem, with a particular focus on vertical profile variations beneath four dominant shrub species (AS-Alhagi sparsifolia, KC-Karelinia caspia, TR- Tamarix ramosissima, CC- Calligonum caput-medusae). Utilizing comprehensive soil sampling and metagenomics techniques, we reveal the diversity and distribution patterns of soil animal communities from the soil surface down to deeper layers (0-100 cm). Our research outcomes have unveiled that Nematoda and Arthropoda emerge as the most predominant classes of soil animals across all studied shrubs. Specifically, Nematoda exhibited notably high abundance in the KC area, while Arthropoda thrived predominantly in the TR region. We also observed a linear decrease in Nematoda populations as soil depth increased, consistent among all shrub species. Moreover, the highest Shannon diversity within soil animal communities was recorded in the KC area, underscoring a trend of declining alpha diversity in the AS region and an increase in other shrub areas as soil depth increased. Notably, the zones dominated by CC and TR displayed the highest levels of beta diversity. Our correlation analysis of soil animals and environmental factors has pinpointed soil water content, available phosphorus, and available potassium as the most influential drivers of variations in the top-classified soil animal communities. This study provides insights into soil animals in deserts, supporting future research to preserve these fragile deserts and enhance our understanding of life below the surface in challenging ecosystems.},
}
@article {pmid38975795,
year = {2024},
author = {Padasas-Adalla, CS and Ortega-Kindica, RCM and Dalayap, R and Martinez, JG and Amparado, O and Moneva, CS and Lomelí-Ortega, CO and Tabugo, SR and Balcázar, JL},
title = {Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse (Hippocampus comes).},
journal = {Physiological genomics},
volume = {56},
number = {8},
pages = {590-595},
doi = {10.1152/physiolgenomics.00039.2024},
pmid = {38975795},
issn = {1531-2267},
mesh = {Animals ; *Smegmamorpha/microbiology/genetics ; *Skin/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Metagenomics/methods ; },
abstract = {Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW &amp; NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.},
}
@article {pmid38901353,
year = {2024},
author = {Wei, G and Zhang, Z and Zhao, F and Sang, Y and Regenstein, JM and Zhou, P},
title = {Characteristic aroma compounds during the fermentation of Chinese steamed bread fermented with different starters.},
journal = {Food chemistry},
volume = {457},
number = {},
pages = {140151},
doi = {10.1016/j.foodchem.2024.140151},
pmid = {38901353},
issn = {1873-7072},
mesh = {*Fermentation ; *Bread/analysis/microbiology ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Saccharomyces cerevisiae/metabolism ; *Odorants/analysis ; Flavoring Agents/metabolism/chemistry ; Microbiota ; Gas Chromatography-Mass Spectrometry ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; East Asian People ; },
abstract = {The characteristic aroma compounds of Chinese steamed bread (CSB) fermented with different starters were studied using HS-SPME-GC/MS, aroma recombination and omission experiments. The dynamic changes of the microbiota and their function and metabolites during fermentation were analyzed using metagenomics and non-targeted metabolomics. Forty-nine volatile flavor compounds were identified, while 5 characteristic aroma-active compounds were investigated in CSB fermented with commercial dry yeast (AQ-CSB), and 10 were investigated in CSB fermented with traditional starter (NY-CSB). Microbial structure and function analysis showed that Saccharomyces cerevisiae dominated during AQ-CSB fermentation and contributed >95% to its KEGG pathways, while Pediococcus pentosaceus, unclassified Pediococcus, Lactobacillus plantarum, Lactobacillus brevis and unclassified Lactobacillus were predominant in NY-CSB and together had an ~96% contribution to these pathways. NY-CSB showed higher metabolic activity during fermentation, and the characteristic metabolites were mainly involved in carbohydrate, amino acid and lipid metabolism. The characteristic aroma compounds were identified and increased the understanding of the contributions of the microbiota. This may be useful for designing starter cultures that produce CSB with desirable aroma properties.},
}
@article {pmid39099658,
year = {2024},
author = {Talbot, BM and Clennon, JA and Rakotoarison, MFN and Rautman, L and Durry, S and Ragazzo, LJ and Wright, PC and Gillespie, TR and Read, TD},
title = {Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17805},
pmid = {39099658},
issn = {2167-8359},
mesh = {Animals ; Madagascar ; Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Sympatry ; Rural Population ; Metagenomics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Cheirogaleidae/genetics/microbiology ; },
abstract = {BACKGROUND: Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs).<br><br>METHODS: This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes.<br><br>RESULTS: Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.},
}
@article {pmid38196020,
year = {2024},
author = {Yu, M and Liu, J and Chen, J and Lin, C and Deng, S and Wu, M},
title = {Metagenomic and metabolomic profiling of dried shrimp (Litopenaeus vannamei) prepared by a procedure traditional to the south China coastal area.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {4},
pages = {1307-1319},
pmid = {38196020},
issn = {1618-1905},
support = {2021KCXTD081//Guangdong University Innovation Team Project/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {*Penaeidae/microbiology ; Animals ; China ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Food Handling/methods ; Shellfish/microbiology ; },
abstract = {Sun-drying is a traditional process for preparing dried shrimp in coastal area of South China, but its impacts on nutrition and the formation of flavor-contributory substances in dried shrimp remain largely unknown. This study aimed to examine the effects of the production process on the microbiota and metabolites in dried shrimp. 16S rDNA amplicon sequencing was employed to identify 170 operational taxonomic units (OTUs), with Vibrio, Photobacterium, and Shewanella emerging as the primary pathogenic bacteria in shrimp samples. Lactococcus lactis was identified as the principal potential beneficial microorganism to accrue during the dried shrimp production process and found to contribute significantly to the development of desirable shrimp flavors. LC-MS-based analyses of dried shrimp sample metabolomes revealed a notable increase in compounds associated with unsaturated fatty acid biosynthesis, arachidonic acid metabolism, amino acid biosynthesis, and flavonoid and flavanol biosynthesis throughout the drying process. Subsequent exploration of the relationship between metabolites and bacterial communities highlighted the predominant coexistence of Bifidobacterium, Clostridium, and Photobacterium contributing heterocyclic compounds and metabolites of organic acids and their derivatives. Conversely, Arthrobacter and Staphylococcus were found to inhibit each other, primarily in the presence of heterocyclic compounds. This comprehensive investigation provides valuable insights into the dynamic changes in the microbiota and metabolites of dried shrimps spanning different drying periods, which we expect to contribute to enhancing production techniques and safety measures for dried shrimp processing.},
}
@article {pmid38158469,
year = {2024},
author = {Uwaremwe, C and Bao, W and Daoura, BG and Mishra, S and Zhang, X and Shen, L and Xia, S and Yang, X},
title = {Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {4},
pages = {1231-1247},
pmid = {38158469},
issn = {1618-1905},
mesh = {*Fusarium/genetics/classification/isolation &amp; purification/pathogenicity ; *Rhizosphere ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Plant Roots/microbiology ; *Rhizopus/genetics/classification/isolation &amp; purification/growth &amp; development ; *Euphorbiaceae/microbiology ; Mycobiome ; Seedlings/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss.<br><br>METHODS: In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection.<br><br>RESULTS: Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification.<br><br>CONCLUSIONS: Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.},
}
@article {pmid37731336,
year = {2024},
author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A},
title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.},
journal = {Critical reviews in biotechnology},
volume = {44},
number = {6},
pages = {1164-1182},
doi = {10.1080/07388551.2023.2254933},
pmid = {37731336},
issn = {1549-7801},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; },
abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.},
}
@article {pmid39096906,
year = {2024},
author = {Giolai, M and Verweij, W and Martin, S and Pearson, N and Nicholson, P and Leggett, RM and Clark, MD},
title = {Measuring air metagenomic diversity in an agricultural ecosystem.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.07.030},
pmid = {39096906},
issn = {1879-0445},
abstract = {All species shed DNA during life or in death, providing an opportunity to monitor biodiversity via environmental DNA (eDNA). In recent years, combining eDNA, high-throughput sequencing technologies, bioinformatics, and increasingly complete sequence databases has promised a non-invasive and non-destructive environmental monitoring tool. Modern agricultural systems are often large monocultures and so are highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is key for efficient and early disease prevention, lower pesticide use, and better food security. Although the air is rich in biodiversity, it has the lowest DNA concentration of all environmental media and yet is the route for windborne spread of many damaging crop pathogens. Our work suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. Here, we show that the airborne DNA of microbes can be recovered, shotgun sequenced, and taxonomically classified, including down to the species level. We show that by monitoring a field growing key crops we can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months, often correlating with weather variables. We add to the evidence that aerial eDNA can be used as a source for biomonitoring in terrestrial ecosystems, specifically highlighting agriculturally relevant species and how pathogen levels correlate with weather conditions. Our ability to detect dynamically changing levels of species and strains highlights the value of airborne eDNA in agriculture, monitoring biodiversity changes, and tracking taxa of interest.},
}
@article {pmid38810936,
year = {2024},
author = {Cho, Y and Park, K and Park, J and An, J and Myung, H and Yoon, H},
title = {Exploring the therapeutic potential of endolysin CD27L_EAD against Clostridioides difficile infection.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {2},
pages = {107222},
doi = {10.1016/j.ijantimicag.2024.107222},
pmid = {38810936},
issn = {1872-7913},
mesh = {*Clostridioides difficile/drug effects/genetics ; *Endopeptidases/pharmacology/genetics/therapeutic use ; *Clostridium Infections/drug therapy/microbiology ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Bacteriophages/genetics ; Bacteriolysis/drug effects ; },
abstract = {OBJECTIVES: Clostridioides difficile has emerged as a major cause of life-threatening diarrheal disease. Conventional antibiotics used in current standards of care exacerbate the emergence of antibiotic-resistant strains and pose a risk of recurrent C. difficile infection (CDI). Thus, there is an urgent need for alternative therapeutics that selectively eliminate C. difficile without disturbing the commensal microbiota. This study aimed to explore the potential of endolysins as an alternative therapeutic agent to antibiotics. Endolysin is a bacteriophage-derived peptidoglycan hydrolase that aids in the release of phage progeny during the final stage of infection.<br><br>METHODS: In order to exploit endolysin as a therapeutic agent against CDI, the bactericidal activity of 23 putative endolysins was compared and &#x3a6;CD27 endolysin CD27L was selected and modified to CD27L_EAD by cleaving the cell-wall binding domain of CD27L.<br><br>RESULTS: CD27L_EAD exhibited greater bacteriolytic activity than CD27L and its activity was stable over a wide range of salt concentrations and pH conditions. CD27L_EAD was added to a co-culture of human gut microbiota with C. difficile and the bacterial community structure was analyzed. CD27L_EAD did not impair the richness and diversity of the bacterial population but remarkably attenuated the abundance of C. difficile. Furthermore, the co-administration of vancomycin exerted synergistic bactericidal activity against C. difficile. &#x3b2;-diversity analysis revealed that CD27L_EAD did not significantly disturb the composition of the microbial community, whereas the abundance of some species belonging to the family Lachnospiraceae decreased after CD27L_EAD treatment.<br><br>CONCLUSIONS: This study provides insights into endolysin as a prospective therapeutic agent for the treatment of CDI without damaging the normal gut microbiota.},
}
@article {pmid39095404,
year = {2024},
author = {De Filippis, F and Valentino, V and Yap, M and Cabrera-Rubio, R and Barcenilla, C and Carlino, N and Cobo-Díaz, JF and Quijada, NM and Calvete-Torre, I and Ruas-Madiedo, P and Sabater, C and Sequino, G and Pasolli, E and Wagner, M and Margolles, A and Segata, N and Álvarez-Ordóñez, A and Cotter, PD and Ercolini, D},
title = {Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {67},
pmid = {39095404},
issn = {2055-5008},
support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Probiotics ; *Cheese/microbiology ; Metagenome ; Food Microbiology ; Microbiota ; Humans ; Dairying/methods ; Europe ; Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin.},
}
@article {pmid39094393,
year = {2024},
author = {Turco, S and Brugneti, F and Giubilei, I and Silvestri, C and Petrović, M and Drais, MI and Cristofori, V and Speranza, S and Mazzaglia, A and Contarini, M and Rossini, L},
title = {A bud's life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity.},
journal = {Microbiological research},
volume = {287},
number = {},
pages = {127851},
doi = {10.1016/j.micres.2024.127851},
pmid = {39094393},
issn = {1618-0623},
abstract = {Despite Corylus avellana L. being an economically important shrub species known for its resilience to adverse environmental conditions, it constantly faces attacks from a plethora of biotic entities. Among these, the mite pest Phytoptus avellanae is gaining importance, causing economic losses every year. This mite colonises the new generative and vegetative buds, leading them to become swollen and reddish, and drastically reducing hazelnut production. The biology behind gall formation is still poorly understood. This study provides a qualitative and quantitative description of the microbiome in both healthy and infested buds of two economically important hazelnut cultivars through metabarcoding of fungal ITS and bacterial 16 S. Potentially pathogenic genera such as Fusarium and Pseudomonas were predominant in the infested buds, along with the obligate intracellular bacterial genus Wolbachia. Akanthomyces muscarius was instead isolated from culture-based methods only from the infested buds. These findings could improve the understanding of gall ecology, supporting the management of mite populations, and they could also serve as a milestone for further studies on low-impact, monitoring-driven, and genetically targeted control strategies.},
}
@article {pmid38945961,
year = {2024},
author = {Kim, N and Ma, J and Kim, W and Kim, J and Belenky, P and Lee, I},
title = {Genome-resolved metagenomics: a game changer for microbiome medicine.},
journal = {Experimental &amp; molecular medicine},
volume = {56},
number = {7},
pages = {1501-1512},
pmid = {38945961},
issn = {2092-6413},
support = {HI19C1344//Korea Health Industry Development Institute (KHIDI)/ ; R01 DK125382/DK/NIDDK NIH HHS/United States ; R01 DK125382/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Bacteria/genetics/classification ; Animals ; Genome, Bacterial ; Gastrointestinal Microbiome/genetics ; },
abstract = {Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.},
}
@article {pmid39092808,
year = {2024},
author = {Jokela, R and Pärnänen, KM and Ponsero, AJ and Lahti, L and Kolho, KL and de Vos, WM and Salonen, A},
title = {A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2383746},
doi = {10.1080/19490976.2024.2383746},
pmid = {39092808},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Female ; *Feces/microbiology ; Male ; Cohort Studies ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Infant, Newborn ; Bacteroides/genetics/drug effects/growth &amp; development ; Child, Preschool ; Metagenome ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.},
}
@article {pmid39091712,
year = {2024},
author = {Qu, B and Li, Z},
title = {Exploring non-invasive diagnostics for metabolic dysfunction-associated fatty liver disease.},
journal = {World journal of gastroenterology},
volume = {30},
number = {28},
pages = {3447-3451},
doi = {10.3748/wjg.v30.i28.3447},
pmid = {39091712},
issn = {2219-2840},
mesh = {Humans ; *Biomarkers/blood/analysis/metabolism ; *Non-alcoholic Fatty Liver Disease/diagnosis/blood/metabolism ; *Liver/pathology/metabolism ; Biopsy ; Liver Cirrhosis/diagnosis/blood/pathology ; Disease Progression ; Feces/chemistry ; Algorithms ; Gastrointestinal Microbiome ; Metagenome ; },
abstract = {The population with metabolic dysfunction-associated fatty liver disease (MAFLD) is increasingly common worldwide. Identification of people at risk of progression to advanced stages is necessary to timely offer interventions and appropriate care. Liver biopsy is currently considered the gold standard for the diagnosis and staging of MAFLD, but it has associated risks and limitations. This has spurred the exploration of non-invasive diagnostics for MAFLD, especially for steatohepatitis and fibrosis. These non-invasive approaches mostly include biomarkers and algorithms derived from anthropometric measurements, serum tests, imaging or stool metagenome profiling. However, they still need rigorous and widespread clinical validation for the diagnostic performance.},
}
@article {pmid39091676,
year = {2024},
author = {Li, Y and Mao, X and Shi, P and Wan, Z and Yang, D and Ma, T and Wang, B and Wang, J and Wang, J and Zhu, R},
title = {Microbiome-host interactions in the pathogenesis of acute exacerbation of chronic obstructive pulmonary disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1386201},
doi = {10.3389/fcimb.2024.1386201},
pmid = {39091676},
issn = {2235-2988},
mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; Humans ; *Microbiota ; Female ; Male ; Aged ; *Sputum/microbiology ; Middle Aged ; Haemophilus influenzae/genetics ; Computational Biology ; Host Microbial Interactions ; Metagenomics ; Disease Progression ; Bacteria/classification/genetics/isolation &amp; purification ; Signal Transduction ; Host-Pathogen Interactions ; },
abstract = {OBJECTIVE: To explore the underlying mechanisms the airway microbiome contributes to Acute Exacerbation of Chronic Obstructive Pulmonary Disease(AECOPD).<br><br>METHODS: We enrolled 31 AECOPD patients and 26 stable COPD patients, their sputum samples were collected for metagenomic and RNA sequencing, and then subjected to bioinformatic analyses. The expression of host genes was validated by Quantitative Real-time PCR(qPCR) using the same batch of specimens.<br><br>RESULTS: Our results indicated a higher expression of Rothia mucilaginosa(p=0.015) in the AECOPD group and Haemophilus influenzae(p=0.005) in the COPD group. The Different expressed genes(DEGs) detected were significantly enriched in "type I interferon signaling pathway"(p<0.001, q=0.001) in gene function annotation, and "Cytosolic DNA-sensing pathway"(p=0.002, q=0.024), "Toll-like receptor signaling pathway"(p=0.006, q=0.045), and "TNF signaling pathway"(p=0.006, q=0.045) in KEGG enrichment analysis. qPCR amplification experiment verified that the expression of OASL and IL6 increased significantly in the AECOPD group.<br><br>CONCLUSION: Pulmonary bacteria dysbiosis may regulate the pathogenesis of AECOPD through innate immune system pathways like type I interferon signaling pathway and Toll-like receptor signaling pathway.},
}
@article {pmid39090708,
year = {2024},
author = {Stiffler, AK and Hesketh-Best, PJ and Varona, NS and Zagame, A and Wallace, BA and Lapointe, BE and Silveira, CB},
title = {Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {143},
pmid = {39090708},
issn = {2049-2618},
support = {2023349872//National Science Foundation/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; 80NSSC23K0676/NASA/NASA/United States ; },
mesh = {*Sargassum/microbiology ; *Symbiosis ; *Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; *Seawater/microbiology/virology ; Genome, Viral ; Metagenome ; Bacteria/virology/genetics/classification ; Genomics ; Microbiota ; Phylogeny ; Genome, Bacterial ; Synechococcus/virology/genetics ; },
abstract = {BACKGROUND: Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Yet, how viruses that infect bacteria (phages) influence these bacteria-eukaryote interactions is still largely unknown. Here, we investigate the role of viruses on the genomic diversity and functional adaptations of bacteria associated with pelagic sargassum. This brown alga has dramatically increased its distribution range in the Atlantic in the past decade and is predicted to continue expanding, imposing severe impacts on coastal ecosystems, economies, and human health.<br><br>RESULTS: We reconstructed 73 bacterial and 3963 viral metagenome-assembled genomes (bMAGs and vMAGs, respectively) from coastal Sargassum natans VIII and surrounding seawater. S. natans VIII bMAGs were enriched in prophages compared to seawater (28% and 0.02%, respectively). Rhodobacterales and Synechococcus bMAGs, abundant members of the S. natans VIII microbiome, were shared between the algae and seawater but were associated with distinct phages in each environment. Genes related to biofilm formation and quorum sensing were enriched in S. natans VIII phages, indicating their potential to influence algal association in their bacterial hosts. In-vitro assays with a bacterial community harvested from sargassum surface biofilms and depleted of free viruses demonstrated that these bacteria are protected from lytic infection by seawater viruses but contain intact and inducible prophages. These bacteria form thicker biofilms when growing on sargassum-supplemented seawater compared to seawater controls, and phage induction using mitomycin C was associated with a significant decrease in biofilm formation. The induced metagenomes were enriched in genomic sequences classified as temperate viruses compared to uninduced controls.<br><br>CONCLUSIONS: Our data shows that prophages contribute to the flexible genomes of S. natans VIII-associated bacteria. These prophages encode genes with symbiotic functions, and their induction decreases biofilm formation, an essential capacity for flexible symbioses between bacteria and the alga. These results indicate that prophage acquisition and induction contribute to genomic and functional diversification during sargassum-bacteria symbioses, with potential implications for algae growth. Video Abstract.},
}
@article {pmid39090559,
year = {2024},
author = {Sime, AM and Kifle, BA and Woldesemayat, AA and Gemeda, MT},
title = {Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {285},
pmid = {39090559},
issn = {1471-2180},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Forests ; *Bacteria/genetics/enzymology/classification/isolation &amp; purification ; Ethiopia ; *Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Microbiota/genetics ; Biodiversity ; Soil/chemistry ; Metagenome ; Biofuels ; Bacterial Proteins/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Carbohydrate Metabolism ; },
abstract = {BACKGROUND: The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.<br><br>RESULTS: The microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as &#x3b2;-glucosidase, endo-&#x3b2;-1,4-mannanase, exo-&#x3b2;-1,4-glucanase, &#x3b1;-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family.<br><br>CONCLUSIONS: In general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.},
}
@article {pmid39029911,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {Metatranscriptomics: A Tool for Clinical Metagenomics.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {8},
pages = {394-407},
doi = {10.1089/omi.2024.0130},
pmid = {39029911},
issn = {1557-8100},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; },
abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.},
}
@article {pmid38864950,
year = {2024},
author = {Ortega-Kindica, RCMH and Padasas-Adalla, CS and Tabugo, SRM and Martinez, JGT and Amparado, OA and Moneva, CSO and Dalayap, R and Lomeli-Ortega, CO and Balcazar, JL},
title = {Shotgun Metagenomics Reveals Taxonomic and Functional Patterns of the Microbiome Associated with Barbour's Seahorse (Hippocampus barbouri).},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {26},
number = {4},
pages = {835-841},
pmid = {38864950},
issn = {1436-2236},
mesh = {Animals ; *Smegmamorpha/microbiology ; *Metagenomics ; *Skin/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/metabolism ; *Microbiota/genetics ; },
abstract = {This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour's seahorse (Hippocampus barbouri) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour's seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives.},
}
@article {pmid38315309,
year = {2024},
author = {Macharoen, P and Mhuantong, W and Wannawong, T and Leesutthiphonchai, W and Tanasupawat, S and Suwannarach, N and Kuncharoen, N},
title = {Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand.},
journal = {Folia microbiologica},
volume = {69},
number = {4},
pages = {941-952},
pmid = {38315309},
issn = {1874-9356},
support = {N42A650203//National Research Council of Thailand/ ; },
mesh = {*Solanum tuberosum/microbiology ; Thailand ; *Plant Tubers/microbiology ; *Plant Diseases/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Food Storage ; Biodiversity ; Temperature ; Phylogeny ; Microbiota ; DNA, Bacterial/genetics ; Metagenomics ; },
abstract = {Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.},
}
@article {pmid39090215,
year = {2024},
author = {Boscari, E and Palle, SD and Vitulo, N and Scapolatiello, A and Schiavon, L and Cariani, A and Papetti, C and Zane, L and Marino, IAM and Congiu, L},
title = {MIPs: multi-locus intron polymorphisms in species identification and population genomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17870},
pmid = {39090215},
issn = {2045-2322},
support = {256475//FSBI Small Research Grants (Fishery Society of the Britisk Isles)/ ; 622320//European Marie Curie Project "Polarexpress"/ ; 164793//University of Padova BIRD/ ; 2016_00307//Italian National Programme of Antarctic Research (PNRA)/ ; CN00000033//NBFC to University of Padova/ ; },
mesh = {Animals ; *Introns/genetics ; *Fishes/genetics/classification ; Polymorphism, Single Nucleotide ; Genetics, Population ; Species Specificity ; Metagenomics/methods ; Genomics/methods ; },
abstract = {The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.},
}
@article {pmid39088249,
year = {2024},
author = {Haring, VC and Litz, B and Jacob, J and Brecht, M and Bauswein, M and Sehl-Ewert, J and Heroldova, M and Wylezich, C and Hoffmann, D and Ulrich, RG and Beer, M and Pfaff, F},
title = {Detection of novel orthoparamyxoviruses, orthonairoviruses and an orthohepevirus in European white-toothed shrews.},
journal = {Microbial genomics},
volume = {10},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001275},
pmid = {39088249},
issn = {2057-5858},
mesh = {Animals ; *Shrews/virology ; *Phylogeny ; Genome, Viral ; Europe ; Paramyxoviridae/genetics/isolation &amp; purification/classification ; Metagenomics ; Virome/genetics ; RNA, Viral/genetics ; Humans ; },
abstract = {While the viromes and immune systems of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores (order Eulipotyphla) despite their wide geographic distribution. Anthropogenic land use and outdoor recreational activities, as well as changes in the range of shrews, may lead to an expansion of the human-shrew interface with the risk of spillover infections, as reported for Borna disease virus 1. We investigated the virome of 45 individuals of 4 white-toothed shrew species present in Europe, using metagenomic RNA sequencing of tissue and intestine pools. Moderate to high abundances of sequences related to the families Paramyxoviridae, Nairoviridae, Hepeviridae and Bornaviridae were detected. Whole genomes were determined for novel orthoparamyxoviruses (n=3), orthonairoviruses (n=2) and an orthohepevirus. The novel paramyxovirus, tentatively named Hasua virus, was phylogenetically related to the zoonotic Langya virus and Mòjiāng virus. The novel orthonairoviruses, along with the potentially zoonotic Erve virus, fall within the shrew-borne Thiafora virus genogroup. The highest viral RNA loads of orthoparamyxoviruses were detected in the kidneys, in well-perfused organs for orthonairoviruses and in the liver and intestine for orthohepevirus, indicating potential transmission routes. Notably, several shrews were found to be coinfected with viruses from different families. Our study highlights the virus diversity present in shrews, not only in biodiversity-rich regions but also in areas influenced by human activity. This study warrants further research to characterize and assess the clinical implications and risk of these viruses and the importance of shrews as reservoirs in European ecosystems.},
}
@article {pmid39088170,
year = {2024},
author = {Mukherjee, P and Sharma, RS and Mishra, V},
title = {Deciphering the ecological impact of azo dye pollution through microbial community analysis in water-sediment microcosms.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39088170},
issn = {1614-7499},
abstract = {The uncontrolled release of untreated dyeing wastewater into aquatic ecosystems poses global environmental risks. It alters native microbial communities and associated ecological processes, often going unnoticed. Therefore, the influence of acid orange 7 dye (AO7) contamination on the natural microbial community was investigated using a water-sediment microcosm. Compared to sterile microcosms, complete dye decolourization in natural microcosms showed microbial communities' significance in combating xenobiotic contamination. Proteobacteria dominated the water community, whereas Firmicutes dominated the sediment. AO7 exposure induced notable shifts in the structural composition of the bacterial community in both water and sediment. Niveispirillum exhibited a marked decrease, and Pseudomonas demonstrated a notable increase. The - 9.0 log2FC in Niveispirillum, a nitrogen-fixing bacterium, from 24.4% in the control to 0.1% post-treatment, may disrupt nutrient balance, plant growth, and ecosystem productivity. Conversely, elevated levels of Pseudomonas sp. resulting from azo dye exposure demonstrate its ability to tolerate and bioremediate organic pollutants, highlighting its resilience. Functional profiling via KEGG pathway analysis revealed differential expression patterns under AO7 stress. Specifically, valine, leucine, and isoleucine degradation pathways in water decreased by 52.2%, and cysteine and methionine metabolism ceased expression entirely, indicating reduced protein metabolism and nutrient bioavailability under dye exposure. Furthermore, in sediment, glutathione metabolism ceased, indicating increased oxidative stress following AO7 infusion. However, C5-branched dibasic acid metabolism and limonene and pinene degradation were uniquely expressed in sediment. Decreased methane metabolism exacerbates the effects of global warming on aquatic ecosystems. Further, ceased-butanoate metabolic pathways reflect the textile dye wastewater-induced adverse impact on ecological processes, such as organic matter decomposition, energy flow, nutrient cycling, and community dynamics that help maintain self-purification and ecological balance in river ecosystems. These findings underscore the critical need for more comprehensive environmental monitoring and management strategies to mitigate ecological risks posed by textile dyes in aquatic ecosystems, which remain unnoticed.},
}
@article {pmid39086173,
year = {2024},
author = {Hu, A and Zhao, W and Wang, J and Qi, Q and Xiao, X and Jing, H},
title = {Microbial communities reveal niche partitioning across the slope and bottom zones of the challenger deep.},
journal = {Environmental microbiology reports},
volume = {16},
number = {4},
pages = {e13314},
doi = {10.1111/1758-2229.13314},
pmid = {39086173},
issn = {1758-2229},
support = {SL2021PT103//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 91751116//Training Program of the Major Research Plan of the National Natural Science Foundation of China/ ; ZDKJ2021036//Hainan Province Science and Technology Special Fund/ ; 41921006//National Natural Science Foundation of China/ ; 42106087//National Natural Science Foundation of China/ ; },
mesh = {*Seawater/microbiology ; *Microbiota ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics ; Metagenome ; Archaea/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {Widespread marine microbiomes exhibit compositional and functional differentiation as a result of adaptation driven by environmental characteristics. We investigated the microbial communities in both seawater and sediments on the slope (7-9 km) and the bottom (9-11 km) of the Challenger Deep of the Mariana Trench to explore community differentiation. Both metagenome-assembled genomes (MAGs) and 16S rRNA amplicon sequence variants (ASVs) showed that the microbial composition in the seawater was similar to that of sediment on the slope, while distinct from that of sediment in the bottom. This scenario suggested a potentially stronger community interaction between seawater and sediment on the slope, which was further confirmed by community assembly and population movement analyses. The metagenomic analysis also indicates a specific stronger potential of nitrate reduction and sulphate assimilation in the bottom seawater, while more versatile nitrogen and sulphur cycling pathways occur on the slope, reflecting functional differentiations among communities in conjunction with environmental features. This work implies that microbial community differentiation occurred in the different hadal niches, and was likely an outcome of microbial adaptation to the extreme hadal trench environment, especially the associated hydrological and geological conditions, which should be considered and measured in situ in future studies.},
}
@article {pmid38987594,
year = {2024},
author = {Fujimoto, K and Hayashi, T and Yamamoto, M and Sato, N and Shimohigoshi, M and Miyaoka, D and Yokota, C and Watanabe, M and Hisaki, Y and Kamei, Y and Yokoyama, Y and Yabuno, T and Hirose, A and Nakamae, M and Nakamae, H and Uematsu, M and Sato, S and Yamaguchi, K and Furukawa, Y and Akeda, Y and Hino, M and Imoto, S and Uematsu, S},
title = {An enterococcal phage-derived enzyme suppresses graft-versus-host disease.},
journal = {Nature},
volume = {632},
number = {8023},
pages = {174-181},
pmid = {38987594},
issn = {1476-4687},
mesh = {Adult ; Aged ; Animals ; Female ; Humans ; Male ; Mice ; Middle Aged ; Young Adult ; *Bacteriophages/enzymology/genetics ; Biofilms/drug effects/growth &amp; development ; Dysbiosis/complications/microbiology ; *Enterococcus faecalis/drug effects/genetics/growth &amp; development/metabolism/virology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Germ-Free Life ; *Graft vs Host Disease/complications/microbiology/prevention &amp; control/therapy ; Hematopoietic Stem Cell Transplantation/adverse effects ; In Vitro Techniques ; Intestines/drug effects/microbiology ; Perforin/metabolism ; Risk Factors ; Transplantation, Homologous/adverse effects ; Whole Genome Sequencing ; Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Changes in the gut microbiome have pivotal roles in the pathogenesis of acute graft-versus-host disease (aGVHD) after allogenic haematopoietic cell transplantation (allo-HCT)[1-6]. However, effective methods for safely resolving gut dysbiosis have not yet been established. An expansion of the pathogen Enterococcus faecalis in the intestine, associated with dysbiosis, has been shown to be a risk factor for aGVHD[7-10]. Here we analyse the intestinal microbiome of patients with allo-HCT, and find that E. faecalis escapes elimination and proliferates in the intestine by forming biofilms, rather than by acquiring drug-resistance genes. We isolated cytolysin-positive highly pathogenic E. faecalis from faecal samples and identified an anti-E. faecalis enzyme derived from E. faecalis-specific bacteriophages by analysing bacterial whole-genome sequencing data. The antibacterial enzyme had lytic activity against the biofilm of E. faecalis in vitro and in vivo. Furthermore, in aGVHD-induced gnotobiotic mice that were colonized with E. faecalis or with patient faecal samples characterized by the domination of Enterococcus, levels of intestinal cytolysin-positive E. faecalis were decreased and survival was significantly increased in the group that was treated with the E. faecalis-specific enzyme, compared with controls. Thus, administration of a phage-derived antibacterial enzyme that is specific to biofilm-forming pathogenic E. faecalis-which is difficult to eliminate with existing antibiotics-might provide an approach to protect against aGVHD.},
}
@article {pmid38819818,
year = {2024},
author = {Zhao, J and Zhou, X and Qiu, Y and Jia, R},
title = {Characterization of the gut butyrate-producing bacteria and lipid metabolism in African green monkey as a natural host of simian immunodeficiency virus infection.},
journal = {AIDS (London, England)},
volume = {38},
number = {11},
pages = {1617-1626},
doi = {10.1097/QAD.0000000000003944},
pmid = {38819818},
issn = {1473-5571},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; *Simian Acquired Immunodeficiency Syndrome/metabolism/virology ; *Lipid Metabolism ; *Feces/microbiology ; Chlorocebus aethiops ; *Macaca mulatta ; Bacteria/classification/isolation &amp; purification/metabolism ; Simian Immunodeficiency Virus ; Metagenomics ; Metabolomics ; Macaca fascicularis ; },
abstract = {OBJECTIVE: Natural hosts of simian immunodeficiency virus (SIV), such as the African green monkey (AGM), possess the ability to avoid acquired immune deficiency syndrome (AIDS) despite lifelong infection. The underlying mechanisms are not completely understood. This study aimed to characterize the gut microbiome and metabolite profiles of different nonhuman primates (NHPs) to provide potential insight into AIDS resistance.<br><br>DESIGN AND METHODS: Fresh feces from Cynomolgus macaques (CMs), and Rhesus macaques (RMs), SIV- AGMs (AGM_N), and SIV+ AGMs (AGM_P) were collected and used for metagenomic sequencing and metabonomic analysis.<br><br>RESULTS: Compared with CMs and RMs, significant decreases in the abundances of Streptococcus , Alistipes , Treponema , Bacteroides , and Methanobrevibacter (P &#x200a;<&#x200a;0.01), and significant increases in the abundances of Clostridium , Eubacterium , Blautia , Roseburia , Faecalibacterium , and Dialister (P &#x200a;<&#x200a;0.01) were detected in AGM_N. Compared with AGM_N, a trend toward increased abundances of Streptococcus and Roseburia were found in AGM_P. The levels of metabolites involved in lipid metabolism and butanoate metabolism significantly differed among AGM_P, AGM_N and CM (P &#x200a;<&#x200a;0.05).<br><br>CONCLUSIONS: Our data, for the first time, demonstrated distinguishing features in the abundances of butyrate-producing bacteria and lipid metabolism capacities between different NHP hosts of SIV infection. These findings may correlate with the different characteristics observed among these hosts in the maintenance of intestinal epithelial barrier integrity, regulation of inflammation, and provide insights into AIDS resistance in AGMs.},
}
@article {pmid38776961,
year = {2024},
author = {Remaks, JD and Vientos-Plotts, AI and Rindt, H and McAdams, Z and Ericsson, AC and Reinero, CR},
title = {Multistrain probiotics fail to modulate the asthmatic phenotype, respiratory microbiota, and immune responses in cats.},
journal = {American journal of veterinary research},
volume = {85},
number = {8},
pages = {},
doi = {10.2460/ajvr.23.12.0271},
pmid = {38776961},
issn = {1943-5681},
mesh = {Animals ; Cats ; *Asthma/veterinary/immunology ; *Probiotics/pharmacology/administration &amp; dosage/therapeutic use ; *Cat Diseases/immunology/microbiology ; Female ; Male ; Microbiota/drug effects ; Bronchoalveolar Lavage Fluid/cytology ; Glucocorticoids/therapeutic use ; Phenotype ; },
abstract = {OBJECTIVE: To determine if multistrain probiotics administered to asthmatic cats treated with anti-inflammatory glucocorticoids would attenuate the asthmatic phenotype and beneficially alter respiratory, blood, and oropharyngeal (OP) microbial communities and immune parameters versus placebo.<br><br>ANIMALS: 13 client-owned asthmatic cats.<br><br>METHODS: A randomized, blinded, placebo-controlled clinical trial of asthmatic cats receiving anti-inflammatory glucocorticoids with oral multistrain probiotics or placebo assessed owner-perceived improvement and airway eosinophilia at baseline and after 2 weeks of treatment. Bronchoalveolar lavage fluid (BALF), blood, OP, and rectal microbial communities were compared using 16S rRNA amplicon sequencing. Real-time PCR for transcription factors, activation markers and cytokines, and IgA ELISAs were evaluated. Statistical analyses used 2-way repeated-measures ANOVA or permutational ANOVA (significance, P < .05).<br><br>RESULTS: After treatment, there were no significant differences in owner-perceived clinical signs or mean &#xb1; SEM BALF eosinophils between groups. There was a significant decrease in rectal &#x3b1;-diversity but not in &#x3b1;- or &#x3b2;-diversity in BALF, blood, or OP between groups or over time. There were no significant differences in CD25, FoxP3, GATA, Helios, IL-4, IL-5, IL-10, IL-13, IL-17, IFN-&#x3b3; mRNA, or serum or BALF IgA between groups or over time.<br><br>CLINICAL RELEVANCE: In asthmatic cats, oral multistrain probiotics failed to improve owner-perceived signs, reduce airway eosinophilia, modify microbial community composition, or alter assessed immune responses versus placebo or over time. Longer treatment, different probiotic composition or delivery (eg, aerosolized), or larger number of cats would represent the next stages of study.},
}
@article {pmid38315959,
year = {2024},
author = {Meldrum, OW and Donaldson, GC and Narayana, JK and Xaverius Ivan, F and Jaggi, TK and Mac Aogáin, M and Finney, LJ and Allinson, JP and Wedzicha, JA and Chotirmall, SH},
title = {Accelerated Lung Function Decline and Mucus-Microbe Evolution in Chronic Obstructive Pulmonary Disease.},
journal = {American journal of respiratory and critical care medicine},
volume = {210},
number = {3},
pages = {298-310},
doi = {10.1164/rccm.202306-1060OC},
pmid = {38315959},
issn = {1535-4970},
support = {020458-00001//LKCMedicine-ICL Fellowship/ ; LEARN008//LKCMedicine LEARN Grant/ ; SGL026/1079//National Heart and Lung Institute (NHLI) Lectureship/ ; MOH-000141//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-000710//National Medical Research Council/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; //National Institute of Health Research (NIHR) Biomedical Research Centre to Imperial College London/ ; //National Institute of Health Research (NIHR) Biomedical Research Centre to Royal Brompton Hospital/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; Male ; Female ; Aged ; Middle Aged ; Prospective Studies ; *Sputum/microbiology ; *Mucus/microbiology ; *Microbiota ; Longitudinal Studies ; Disease Progression ; Mucin-5B/metabolism ; Forced Expiratory Volume ; Mucin 5AC/metabolism ; London ; },
abstract = {Rationale: Progressive lung function loss is recognized in chronic obstructive pulmonary disease (COPD); however, no study concurrently evaluates how accelerated lung function decline relates to mucus properties and the microbiome in COPD. Objectives: Longitudinal assessment of mucus and microbiome changes accompanying accelerated lung function decline in patients COPD. Methods: This was a prospective, longitudinal assessment of the London COPD cohort exhibiting the greatest FEV1 decline (n = 30; accelerated decline; 156 ml/yr FEV1 loss) and with no FEV1 decline (n = 28; nondecline; 49 ml/yr FEV1 gain) over time. Lung microbiomes from paired sputum (total 116 specimens) were assessed by shotgun metagenomics and corresponding mucus profiles evaluated for biochemical and biophysical properties. Measurements and Main Results: Biochemical and biophysical mucus properties are significantly altered in the accelerated decline group. Unsupervised principal component analysis showed clear separation, with mucus biochemistry associated with accelerated decline, whereas biophysical mucus characteristics contributed to interindividual variability. When mucus and microbes are considered together, an accelerated decline mucus-microbiome association emerges, characterized by increased mucin (MUC5AC [mucin 5AC] and MUC5B [mucin 5B]) concentration and the presence of Achromobacter and Klebsiella. As COPD progresses, mucus-microbiome shifts occur, initially characterized by low mucin concentration and transition from viscous to elastic dominance accompanied by the commensals Veillonella, Gemella, Rothia, and Prevotella (Global Initiative for Chronic Obstructive Lung Disease [GOLD] A and B) before transition to increased mucus viscosity, mucins, and DNA concentration together with the emergence of pathogenic microorganisms including Haemophilus, Moraxella, and Pseudomonas (GOLD E). Conclusions: Mucus-microbiome associations evolve over time with accelerated lung function decline, symptom progression, and exacerbations affording fresh therapeutic opportunities for early intervention.},
}
@article {pmid39085298,
year = {2024},
author = {Vidal-Verdú, &#xc0; and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M},
title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {65},
pmid = {39085298},
issn = {2055-5008},
support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.},
}
@article {pmid39085233,
year = {2024},
author = {Essex, M and Millet Pascual-Leone, B and Löber, U and Kuhring, M and Zhang, B and Brüning, U and Fritsche-Guenther, R and Krzanowski, M and Fiocca Vernengo, F and Brumhard, S and Röwekamp, I and Anna Bielecka, A and Lesker, TR and Wyler, E and Landthaler, M and Mantei, A and Meisel, C and Caesar, S and Thibeault, C and Corman, VM and Marko, L and Suttorp, N and Strowig, T and Kurth, F and Sander, LE and Li, Y and Kirwan, JA and Forslund, SK and Opitz, B},
title = {Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {66},
pmid = {39085233},
issn = {2055-5008},
support = {SFB-TR84 A1/A5//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 400667201//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TR84//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TR84//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1365, SFB1470, KFO339//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Project 76251-99//Volkswagen Foundation (VolkswagenStiftung)/ ; Project 76251-99//Volkswagen Foundation (VolkswagenStiftung)/ ; KA1-Co-02 'COVIPA'//Helmholtz Association/ ; KA1-Co-02 'COVIPA'//Helmholtz Association/ ; },
mesh = {Humans ; *COVID-19/microbiology/immunology ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; *Dysbiosis ; Male ; Female ; *SARS-CoV-2 ; Middle Aged ; *Cytokines/blood/metabolism ; Metabolome ; Inflammation ; Kynurenine/metabolism/blood ; Aged ; Adult ; },
abstract = {The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.},
}
@article {pmid39080854,
year = {2024},
author = {Suárez-Moo, P and Haro-Moreno, JM and Rodriguez-Valera, F},
title = {Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome.},
journal = {Environmental microbiology},
volume = {26},
number = {8},
pages = {e16684},
doi = {10.1111/1462-2920.16684},
pmid = {39080854},
issn = {1462-2920},
support = {PID2020-118052GB-I00//Ministerio de Econom&#xed;a, Industria y Competitividad/ ; },
mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism/classification ; *Ammonia/metabolism ; *Metagenome ; *Oxidation-Reduction ; *Genome, Archaeal ; *Seawater/microbiology ; Metagenomics ; Phylogeny ; Genetic Variation ; Genomic Islands ; Biodiversity ; },
abstract = {The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long-reads located within the flexible genomic islands (fGIs) identified by their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third-generation sequencing metagenomics.},
}
@article {pmid39080726,
year = {2024},
author = {Li, X and Liu, S and Wu, H and Li, B and Li, Y and Li, R and Tang, D and Zhang, H},
title = {Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {169},
pmid = {39080726},
issn = {1743-422X},
support = {NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. CI2021A00604//the Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; 82374182//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; NO. 81973722//National Nature Science Foundation of China/ ; },
mesh = {Animals ; *Disease Models, Animal ; Mice ; *Enterovirus/genetics/isolation &amp; purification ; *Metagenomics ; *Metabolomics ; *Diet, High-Fat/adverse effects ; *Coronary Disease/virology/blood ; Male ; Mice, Inbred C57BL ; Enterovirus Infections/virology/blood ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Coronary heart disease (CHD) is a common cardiovascular disease that is associated with altered gut microbiota. Enteroviruses, an essential component of the gut microbiome, may play an important role in disease progression. However, the relationship between enteroviruses and CHD remains unclear. The development of high-throughput sequencing technologies has facilitated research on the interconnections between viruses and disease-related metabolites.<br><br>METHODS AND RESULTS: Mice were fed a high-fat diet (CHD group) or chow diet (Sham group) for 12 weeks, and ligation of the left anterior descending coronary artery was performed at the end of week 8. After 4 weeks, all animals were euthanised. Subsequently, the animals were evaluated for basic haemato-biochemical parameters and cardiac function, and aorta staining was performed. Based on enteroviral metagenomics and serum UPLC-MS/MS metabolomics analyses, we evaluated the association between enteroviral groups and serum metabolites of CHD mouse model. A high-fat diet and coronary ligation enabled the establishment of the CHD mouse model. Notably, the enterovirus spectrum of the sham group was significantly different from that of the CHD group, with 24 viral communities of different family and species classification, such as Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus, exhibiting significant differences. In addition, 731 Differential metabolites were detected in the serum of both groups of mice. Correlation network analysis revealed a close relationship between various metabolites related to lipid metabolism and different viruses, including Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus.<br><br>CONCLUSIONS: An animal model of CHD, characterised by lipid disturbance and myocardial ischaemia, was established using a high-fat diet and ligation of the left anterior descending branch of the coronary artery. Tsarbombavirus, Firehammervirus, Mingyongvirus, and Claudivirus were associated with metabolites in the lipid metabolism pathway. The results indicate that Tsarbombavirus may be the main genus interacting with CHD-related metabolites in mice. Conclusively, the findings of our study provide novel insights into the potential relationship enterovirus groups and metabolites associated with CHD.},
}
@article {pmid39002589,
year = {2024},
author = {Bai, X and Zhong, H and Cui, X and Wang, T and Gu, Y and Li, M and Miao, X and Li, J and Lu, L and Xu, W and Li, D and Sun, J},
title = {Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174734},
doi = {10.1016/j.scitotenv.2024.174734},
pmid = {39002589},
issn = {1879-1026},
mesh = {Animals ; *Feces/microbiology ; *Chickens/microbiology ; Swine ; *Soil Microbiology ; Humans ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; China ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {The ongoing and progressive evolution of antibiotic resistance presents escalating challenges for the clinical management and prevention of bacterial infections. Understanding the makeup of resistance genomes and accurately quantifying the current abundance of antibiotic resistance genes (ARGs) are crucial for assessing the threat of antimicrobial resistance (AMR) to public health. This comprehensive study investigated the distribution and diversity of bacterial community composition, ARGs, and virulence factors (VFs) across human, chicken, pig fecal, and soil microbiomes in various provinces of China. As a result, multidrug resistance was identified across all samples. Core ARGs primarily related to multidrug, MLS (Macrolides-Lincosamide-Streptogramins), and tetracycline resistance were characterized. A significant correlation between ARGs and bacterial taxa was observed, especially in soil samples. Probiotic strains such as Lactobacillus harbored ARGs, potentially contributing to the dissemination of antibiotic resistance. We screened subsets of ARGs from samples from different sources as indicators to assess the level of ARGs contamination in samples, with high accuracy. These results underline the complex relationship between microbial communities, resistance mechanisms, and environmental factors, emphasizing the importance of continued research and monitoring to better understand these dynamics.},
}
@article {pmid38997032,
year = {2024},
author = {Satta, A and Ghiotto, G and Santinello, D and Giangeri, G and Bergantino, E and Modesti, M and Raga, R and Treu, L and Campanaro, S and Zampieri, G},
title = {Synergistic functional activity of a landfill microbial consortium in a microplastic-enriched environment.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174696},
doi = {10.1016/j.scitotenv.2024.174696},
pmid = {38997032},
issn = {1879-1026},
mesh = {*Microplastics ; *Soil Microbiology ; *Microbial Consortia ; *Waste Disposal Facilities ; Soil Pollutants/metabolism ; Microbiota ; Biodegradation, Environmental ; Metagenomics ; Plastics ; },
abstract = {Plastic pollution of the soil is a global issue of increasing concern, with far-reaching impact on the environment and human health. To fully understand the medium- and long-term impact of plastic dispersal in the environment, it is necessary to define its interaction with the residing microbial communities and the biochemical routes of its degradation and metabolization. However, despite recent attention on this problem, research has largely focussed on microbial functional potential, failing to clearly identify collective adaptation strategies of these communities. Our study combines genome-centric metagenomics and metatranscriptomics to characterise soil microbial communities adapting to high polyethylene and polyethylene terephthalate concentration. The microbiota were sampled from a landfill subject to decades-old plastic contamination and enriched through prolonged cultivation using these microplastics as the only carbon source. This approach aimed to select the microorganisms that best adapt to these specific substrates. As a result, we obtained simplified communities where multiple plastic metabolization pathways are widespread across abundant and rare microbial taxa. Major differences were found in terms of expression, which on average was higher in planktonic microbes than those firmly adhered to plastic, indicating complementary metabolic roles in potential microplastic assimilation. Moreover, metatranscriptomic patterns indicate a high transcriptional level of numerous genes in emerging taxa characterised by a marked accumulation of genomic variants, supporting the hypothesis that plastic metabolization requires an extensive rewiring in energy metabolism and thus provides a strong selective pressure. Altogether, our results provide an improved characterisation of the impact of microplastics derived from common plastics types on terrestrial microbial communities and suggest biotic responses investing contaminated sites as well as potential biotechnological targets for cooperative plastic upcycling.},
}
@article {pmid38992765,
year = {2024},
author = {Ng, DZW and Low, A and Tan, AJH and Ong, JH and Kwa, WT and Lee, JWJ and Chan, ECY},
title = {Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model.},
journal = {Chemico-biological interactions},
volume = {399},
number = {},
pages = {111140},
doi = {10.1016/j.cbi.2024.111140},
pmid = {38992765},
issn = {1872-7786},
mesh = {Humans ; *Feces/microbiology ; Kinetics ; *Bile Acids and Salts/metabolism ; Gastrointestinal Microbiome ; Chenodeoxycholic Acid/metabolism ; Models, Biological ; Microbiota ; },
abstract = {Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.},
}
@article {pmid38986711,
year = {2024},
author = {Zhang, Y and Chen, J and Du, M and Ruan, Y and Wang, Y and Guo, J and Yang, Q and Shao, R and Wang, H},
title = {Metagenomic insights into microbial variation and carbon cycling function in crop rotation systems.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174529},
doi = {10.1016/j.scitotenv.2024.174529},
pmid = {38986711},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Carbon Cycle ; *Crops, Agricultural ; Microbiota ; Soil/chemistry ; Carbon/metabolism ; Agriculture/methods ; Bacteria/metabolism ; Metagenomics ; Triticum ; },
abstract = {The decomposition and utilization of plant-derived carbon by microorganisms and carbon fixation are crucial pathways for enhancing soil organic carbon (SOC) storage. However, a gap remains in our understanding of the impact of microorganisms on the decomposition of plant-derived carbon and their capacity for carbon fixation in crop rotation systems. Based on a 12-year experiment with wheat-maize (WM), wheat-cotton (WC), and wheat-soybean (WS) rotations, the microbial communities and carbon cycle function were investigated. The results indicated that WS rotation significantly increased SOC content compared to WM and WC. In addition, a significant increase was observed in microbially available carbon and microbial biomass carbon in the WS soil compared with those in the others. Further analysis of the microbial community factors that influenced SOC content revealed that WS rotation, in contrast to WM rotation, enhanced the diversity and richness of bacteria and fungi. Analysis of microbial carbon decomposition functions revealed an increase in starch, lignin, and hemicellulose decomposition genes in the WS soil compared to the others. The changes in carbon decomposition genes were primarily attributed to six bacterial genera, namely Nocardioides, Agromyces, Microvirga, Skermanella, Anaeromyxobacter, and Arthrobacter, as well as four fungal genera, namely Dendryphion, Staphylotrichum, Apiotrichum, and Abortiporus, which were significantly influenced by the crop rotation systems. In addition, microbial carbon fixation-related genes such as ACAT, IDH1, GAPDH, rpiA, and rbcS were significantly enriched in WS. Species annotation of differential carbon fixation genes identified 18 genera that play a role in soil carbon fixation variation within the crop rotation systems. This study highlights the impact of crop rotation systems on SOC content and alterations in specific microbial communities on carbon cycle function.},
}
@article {pmid38986696,
year = {2024},
author = {Pellegrinetti, TA and Cotta, SR and Feitosa, YB and Melo, PLA and Bieluczyk, W and Silva, AMM and Mendes, LW and Sarmento, H and Camargo, PB and Tsai, SM and Fiore, MF},
title = {The role of microbial communities in biogeochemical cycles and greenhouse gas emissions within tropical soda lakes.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174646},
doi = {10.1016/j.scitotenv.2024.174646},
pmid = {38986696},
issn = {1879-1026},
mesh = {*Lakes/chemistry/microbiology ; *Greenhouse Gases/analysis ; Brazil ; *Microbiota ; *Methane/analysis ; Environmental Monitoring ; Wetlands ; Eutrophication ; Air Pollutants/analysis ; },
abstract = {Although anthropogenic activities are the primary drivers of increased greenhouse gas (GHG) emissions, it is crucial to acknowledge that wetlands are a significant source of these gases. Brazil's Pantanal, the largest tropical inland wetland, includes numerous lacustrine systems with freshwater and soda lakes. This study focuses on soda lakes to explore potential biogeochemical cycling and the contribution of biogenic GHG emissions from the water column, particularly methane. Both seasonal variations and the eutrophic status of each examined lake significantly influenced GHG emissions. Eutrophic turbid lakes (ET) showed remarkable methane emissions, likely due to cyanobacterial blooms. The decomposition of cyanobacterial cells, along with the influx of organic carbon through photosynthesis, accelerated the degradation of high organic matter content in the water column by the heterotrophic community. This process released byproducts that were subsequently metabolized in the sediment leading to methane production, more pronounced during periods of increased drought. In contrast, oligotrophic turbid lakes (OT) avoided methane emissions due to high sulfate levels in the water, though they did emit CO2 and N2O. Clear vegetated oligotrophic turbid lakes (CVO) also emitted methane, possibly from organic matter input during plant detritus decomposition, albeit at lower levels than ET. Over the years, a concerning trend has emerged in the Nhecolândia subregion of Brazil's Pantanal, where the prevalence of lakes with cyanobacterial blooms is increasing. This indicates the potential for these areas to become significant GHG emitters in the future. The study highlights the critical role of microbial communities in regulating GHG emissions in soda lakes, emphasizing their broader implications for global GHG inventories. Thus, it advocates for sustained research efforts and conservation initiatives in this environmentally critical habitat.},
}
@article {pmid38981540,
year = {2024},
author = {Funnicelli, MIG and de Carvalho, LAL and Teheran-Sierra, LG and Dibelli, SC and Lemos, EGM and Pinheiro, DG},
title = {Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174577},
doi = {10.1016/j.scitotenv.2024.174577},
pmid = {38981540},
issn = {1879-1026},
mesh = {*Saccharum/microbiology ; *Bacteria/genetics/classification ; Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Plant Development ; },
abstract = {Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.},
}
@article {pmid38971241,
year = {2024},
author = {Zhu, Y and Yan, S and Chen, X and Li, Y and Xie, S},
title = {Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174531},
doi = {10.1016/j.scitotenv.2024.174531},
pmid = {38971241},
issn = {1879-1026},
mesh = {*Geologic Sediments/virology/chemistry ; *Thallium ; *Rivers/virology ; *Water Pollutants, Chemical/analysis ; Viruses ; China ; Environmental Monitoring ; Microbiota ; },
abstract = {Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.},
}
@article {pmid38244232,
year = {2024},
author = {Wu, IW and Chang, LC and Wu, YL and Yang, HY and Twu, YC and Tsai, PY and Paulus, S and Resnick, R and Chung, WH and Yang, CW and Hsieh, WP and Su, SC},
title = {Gut flora metagenomic analysis coupled with metabolic and deep immune profiling in chronic kidney disease.},
journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association},
volume = {39},
number = {8},
pages = {1333-1343},
doi = {10.1093/ndt/gfae013},
pmid = {38244232},
issn = {1460-2385},
support = {MOST-110-2320-B-182A-012 -MY3//Ministry of Science and Technology/ ; BMRPE97//Chang Gung Memorial Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/microbiology/immunology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Metabolome ; },
abstract = {BACKGROUND: Perturbation of gut microbiota has been linked to chronic kidney disease (CKD), which was correlated with a sophisticated milieu of metabolic and immune dysregulation.<br><br>METHODS: To clarify the underlying host-microbe interaction in CKD, we performed multi-omics measurements, including systems-level gut microbiome, targeted serum metabolome and deep immunotyping, in a cohort of patients and non-CKD controls.<br><br>RESULTS: Our analyses on functional profiles of the gut microbiome showed a decrease in the diversity and abundance of carbohydrate-active enzyme (CAZyme) genes but an increase in the abundance of antibiotic resistance, nitrogen cycling enzyme and virulence factor genes in CKD. Moreover, models generated using measurements of serum metabolites (amino acids, bile acids and short-chain fatty acids) or immunotypes were predictive of renal impairment but less so than many of the functional profiles derived from gut microbiota, with the CAZyme genes being the top-performing model to accurately predict the early stage of diseases. In addition, co-occurrence analyses revealed coordinated host-microbe relationships in CKD. Specifically, the highest fractions of significant correlations were identified with circulating metabolites by several taxonomic and functional profiles of gut microbiome, while immunotype features were moderately associated with the abundance of microbiome-encoded metabolic pathways and serum levels of amino acids (e.g. B cell cluster tryptophan and B cell cluster tryptophan metabolism).<br><br>CONCLUSION: Overall, our multi-omics integration revealed several signatures of systems-level gut microbiome in robust associations with host-microbe co-metabolites and renal function, which may have aetiological and diagnostic implications in CKD.},
}
@article {pmid39080019,
year = {2024},
author = {Gao, FZ and Yao, KS and Tan, LJ and He, LY and Liu, YS and Ying, GG},
title = {Single-/Co-Driving of Tetracycline, Triclocarban and Zinc on Microbial Community, Resistome and Function in the Cyanobacteria-Blooming Freshwater Ecosystem.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {113},
number = {2},
pages = {19},
pmid = {39080019},
issn = {1432-0800},
support = {42030703//National Natural Science Foundation of China/ ; U22A20604//National Natural Science Foundation of China/ ; U1701242//National Natural Science Foundation of China/ ; 2022M711215//Chinese Postdoctoral Science Foundation/ ; },
mesh = {*Cyanobacteria/drug effects/genetics ; *Zinc/toxicity ; *Carbanilides/toxicity ; *Fresh Water/microbiology ; *Water Pollutants, Chemical/toxicity ; *Ecosystem ; Anti-Bacterial Agents/toxicity/pharmacology ; Tetracycline/pharmacology/toxicity ; Microbiota/drug effects ; },
abstract = {Environmental concentrations of antimicrobials can inhibit Cyanobacteria, but little is known about their effects on Cyanobacteria-blooming freshwater ecosystem. Here, a 21 days' outdoor freshwater mesocosm experiment was established to study effects of single and combined tetracycline, triclocarban and zinc at environmental concentrations on microbial community, microbial function and antimicrobial resistance using amplicon- and metagenomic-based methods. Results showed that three chemicals reshaped the microbial community with magnified effects by chemical combinations. Relative abundance of Cyanobacteria was decreased in all chemical groups, especially from 74.5 to 0.9% in combination of three chemicals. Microbial community networks were more simplified after exposure. Proteobacteria and Bacteroidetes predominated in Cyanobacteria-degraded ecosystems, and their relative abundances were significantly correlated with antibiotic resistome, suggesting that they might host antibiotic resistance genes. Notably, relative abundance (copy per 16 S rRNA gene) of total antibiotic resistome reached five to nine folds higher than the initial abundance in chemical-combined groups. The affected antibiotic resistance genes referred to a wide range of antibiotic classes. However, weak effects were detected on biocide/metal resistance and microbial virulence. Three chemicals posed complicated effects on microbial function, some of which had consistent variations across the groups, while some varied greatly in chemical groups. The findings highlight sensitivity of Cyanobacteria-blooming ecosystem to antimicrobials.},
}
@article {pmid39079980,
year = {2024},
author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Wang, ST and Shieh, JJ and Wu, CY},
title = {Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17495},
pmid = {39079980},
issn = {2045-2322},
support = {NSTC 108-2314-B-075A-008//National Science and Technology Council/ ; NSTC 110-2314-B-075A-008//National Science and Technology Council/ ; TCVGH-1106801C//Taichung Veterans General Hospital/ ; TCVGH-1116801C//Taichung Veterans General Hospital/ ; TCVGH-1116802C//Taichung Veterans General Hospital/ ; },
mesh = {Animals ; *Imiquimod/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Interleukin-17/metabolism ; *Fatty Acids, Volatile/metabolism ; Mice ; *Skin/drug effects/pathology/microbiology/metabolism ; *Mice, Inbred C57BL ; Metagenomics/methods ; Psoriasis/drug therapy/chemically induced/microbiology ; Metagenome ; Feces/microbiology ; },
abstract = {Short-chain fatty acids (SCFAs) have been proposed to have anti-inflammatory effects and improve immune homeostasis. We aimed to examine the effects of SCFAs on skin phenotype, systemic inflammation, and gut microbiota in mice with psoriasis-like inflammation. Imiquimod (IMQ)-treated C57BL/6 mice served as the study model. We conducted a metagenomic association study of IMQ-mice treated with SCFAs or anti-IL-17 antibody using whole-genome shotgun sequencing. The associations among SCFA supplements, skin thickness, circulating inflammatory profiles, and fecal microbiota profiles were investigated. The microbiome study was performed using pipelines for phylogenetic analysis, functional gene analysis, and pathway analysis. In IMQ-treated mice, there were increases in skin thickness and splenic weight, as well as unique fecal microbial profiles. SCFAs ameliorated IMQ-induced skin thickening, splenic weight gain, and serum IL-17F levels, with results that were comparable with those receiving anti-IL-17 treatment. IMQ-treated mice receiving SCFAs had greater microbial diversity than mice treated with IMQ alone. SCFAs and anti-IL17 treatment were associated with alteration of gut microbiota, with increased prevalences of Oscillospiraceae and Lachnopiraceae and decreased prevalences of Muribaculaceae and Bacteroides, which have been predicted to be associated with increased glycan degradation, phenylalanine metabolism, and xylene degradation. SCFAs may mitigate IMQ-induced skin thickening and IL-17F levels and alter fecal microbiota profiles in IMQ-treated mice.},
}
@article {pmid39078906,
year = {2024},
author = {Fang, Q and Xie, J and Yin, S and Yin, H and Zhou, D},
title = {Analysis of blood microbiota in patients with adult-onset Still's disease and sepsis by metagenomic next-generation sequencing.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {85},
number = {7},
pages = {1-16},
doi = {10.12968/hmed.2024.0121},
pmid = {39078906},
issn = {1750-8460},
mesh = {Humans ; *Sepsis/microbiology/blood/diagnosis ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; *Still's Disease, Adult-Onset/blood/microbiology/diagnosis ; Adult ; Middle Aged ; *Metagenomics/methods ; Microbiota/genetics ; Diagnosis, Differential ; Biomarkers/blood ; },
abstract = {Aims/Background Adult-onset Still's disease (AOSD) shares similar clinical symptoms with sepsis. Thus, differentiating between AOSD and sepsis presents a great challenge while making diagnosis. This study aimed to analyse the changes in blood microbiota related to AOSD and sepsis using metagenomic next-generation sequencing (mNGS), identify potential biomarkers that distinguish AOSD from sepsis, and explore the diagnostic value of mNGS in differentiation between these two pathological conditions. Methods Clinical data of four AOSD patients and four sepsis patients treated in the Department of Rheumatology and Immunology, The Affiliated Hospital of Xuzhou Medical University between October 2021 and February 2022 were collected. The mNGS diagnostic records of these patients were analysed for microbial correlations in terms of species taxonomic structure and beta diversity by comparing blood microbiota between AOSD and sepsis. The biomarkers with the strongest capability in distinguishing the subgroups were screened using a random forest algorithm. Results There was no statistically significant differences between AOSD patients and sepsis controls in terms of gender and age (p > 0.05). A total of 91 operational taxonomic units (OTUs) were obtained. At the level of phylum, Proteobacteria, Ascomycota and Basidiomycota were present in high abundances in both groups (79.76%, 14.18% and 3.30% vs 54.03%, 32.77% and 5.81%). At the genus level, the abundances of Parainfluenzae, Aspergillus and Ralstonia were the top three highest in the AOSD group (73.88%, 10.92% and 5.48%), while Ralstonia, Aspergillus and Malassezia were ranked as the top three in the sepsis group in term of abundance (48.69%, 27.36% and 5.52%). In beta-diversity analysis, there were advances shown in visual principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) between the AOSD group and sepsis group (p < 0.05), with little significant differences in the analysis of similarities (Anosim) (p > 0.05). Linear discriminant analysis effect size (LEfSe) showed that Mucoromycota, Saccharomycetes, Moraxellales, Mucorales, Xanthomonadales, Saccharomycetales, Acinetobacter, Stenotrophomonas, Yarrowia, Apophysomyces, Acinetobacter johnson, Yarrowia lipolytica, Apophysomyces variabilis and Stenotrophomonas maltophilia were more enriched in sepsis group (p < 0.05). The top five variables with the strongest capability in distinguishing between AOSD and sepsis were Acinetobacter johnsonii, Apophysomyces variabilis, Propionibacterium acnes, Stenotrophomonas maltophilia and Yarrowia lipolytica. Conclusion The blood microorganisms in AOSD were different from sepsis, and mNGS was potential to distinguish between AOSD and sepsis.},
}
@article {pmid39078043,
year = {2024},
author = {Esparteiro, D and Fouquet, G and Courtois, A and Jedraszak, G and Marticho, L and Gourdel, M and Billon-Crossouard, S and Croyal, M and Naassila, M and Nguyen-Khac, E and Marcq, I},
title = {Serum bile acids profiles are altered without change of the gut microbiota composition following a seven-day prednisolone therapy in severe alcoholic hepatitis.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2382767},
doi = {10.1080/19490976.2024.2382767},
pmid = {39078043},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hepatitis, Alcoholic/drug therapy/blood ; Male ; *Feces/microbiology/chemistry ; *Bile Acids and Salts/blood/metabolism ; Middle Aged ; Female ; Retrospective Studies ; *Prednisolone/administration &amp; dosage ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Fatty Acids, Volatile/metabolism/blood ; Carrier Proteins/genetics/blood ; Acute-Phase Proteins/metabolism ; Membrane Glycoproteins/blood/genetics ; Aged ; Metagenomics ; },
abstract = {Severe Alcoholic Hepatitis (sAH) is an acute form of liver injury caused by chronic and heavy alcohol drinking. A one-month corticosteroids course is the only sAH reference treatment, and its interactions with the Gut Microbiota (GM), which is a key contributor to liver injury, remain unknown. To evaluate the evolution of the GM in sAH patients, we retrospectively investigated the composition of the GM of 27 sAH patients at the Amiens University Hospital before (D0) and after (D7) a 7-day corticotherapy course using fecal metagenomics sequencing. We also quantified fecal Short-Chain Fatty Acids (SCFA) and fecal and serum Bile Acids (BA), as well as serum Lipopolysaccharide-Binding Protein (LBP). Overall, the community and taxonomical analyses did not reveal any GM evolution between D0 and D7, nor did the SCFA profiles analysis. However, in serum but not fecal samples, the ratio of glyco-conjugated to tauro-conjugated BA was significantly reduced at D7, independently of the response to treatment, while two BA were enriched in non-responder patients. LBP concentration significantly diminished between D0 and D7, which may indicate an improvement of the gut barrier. The stability of the GM of sAH is interesting in the perspective of new treatments based on GM modulation.},
}
@article {pmid39076360,
year = {2024},
author = {Sandybayev, N and Beloussov, V and Strochkov, V and Solomadin, M and Granica, J and Yegorov, S},
title = {Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection.},
journal = {Royal Society open science},
volume = {11},
number = {7},
pages = {240108},
pmid = {39076360},
issn = {2054-5703},
abstract = {Diagnosis of acute respiratory infections (ARIs) is challenging due to the broad diversity of potential microbial causes. We used metagenomic next-generation sequencing (mNGS) to analyze the nasopharyngeal virome of ARI patients, who had undergone testing with a clinical multiplex PCR panel (Amplisens ARVI-screen-FRT). We collected nasopharyngeal swabs from 49 outpatient adults, 32 of whom had ARI symptoms and were PCR-positive, and 4 asymptomatic controls in Kazakhstan during Spring 2021. We assessed the biodiversity of the mNGS-derived virome and concordance with PCR results. PCR identified common ARI viruses in 65% of the symptomatic cases. mNGS revealed viral taxa consisting of human, non-human eukaryotic and bacteriophage groups, comprising 15, 11 and 28 genera, respectively. Notable ARI-associated human viruses included rhinovirus (16.3%), betaherpesvirus 7 (14.3%) and Epstein-Barr virus (8.16%). The primary phage hosts were Streptococcus spp. (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). In total, 47% of ARIs were linked solely to bacterial pathogens, a third to viral-bacterial co-infections, and less than 10% to only viral infections by mNGS. PCR showed low concordance with mNGS, except for rhinovirus. These results underscore the importance of broad diagnostic methods and question the effectiveness of commonly used PCR panels in ARI diagnosis.},
}
@article {pmid39075388,
year = {2024},
author = {Bars-Cortina, D and Ramon, E and Rius-Sansalvador, B and Guinó, E and Garcia-Serrano, A and Mach, N and Khannous-Lleiffe, O and Saus, E and Gabaldón, T and Ibáñez-Sanz, G and Rodríguez-Alonso, L and Mata, A and García-Rodríguez, A and Obón-Santacana, M and Moreno, V},
title = {Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {730},
pmid = {39075388},
issn = {1471-2164},
support = {CD21/00094//Instituto de Salud Carlos III/ ; FI21/00056//Instituto de Salud Carlos III/ ; FI19/00221//Instituto de Salud Carlos III/ ; IMPACT Grant IMP/00019//Instituto de Salud Carlos III/ ; 874662//Horizon 2020/ ; ERC-2016-724173//Horizon 2020/ ; FPU2020-02907//Spanish Ministerio de Universidades/ ; PID2021-126067NB-I00//Spanish Ministry of Science and Innovation for grants/ ; PDC2022-133266-I00//Spanish Ministry of Science and Innovation/ ; SGR01551//Catalan Research Agency/ ; GBMF9742//Gordon and Betty Moore Foundation/ ; LCF/PR/HR21/00737//"La Caixa" foundation/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; Male ; Metagenome ; Female ; },
abstract = {BACKGROUND: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.<br><br>RESULTS: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra.<br><br>CONCLUSIONS: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.},
}
@article {pmid39020259,
year = {2024},
author = {Song, X and Fu, X and Niu, S and Wang, P and Qi, J and Shi, S and Chang, H and Bai, W},
title = {Exploring the effects of Saorilao-4 on the gut microbiota of pulmonary fibrosis model rats based on 16S rRNA sequencing.},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae178},
pmid = {39020259},
issn = {1365-2672},
support = {2024MS08025//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 202202226//Inner Mongolia Health Science and Technology Project/ ; wskjjk2022065//Baotou Health Science and Technology Program/ ; BYJJ-DXK 2022047//Baotou Medical College Young Science and Technology Talent Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *RNA, Ribosomal, 16S/genetics ; Rats ; *Pulmonary Fibrosis/microbiology/genetics ; *Feces/microbiology ; *Disease Models, Animal ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Rats, Sprague-Dawley ; },
abstract = {AIMS: Pulmonary fibrosis (PF) is a progressive and incurable lung disease for which treatment options are limited. Here, we aimed to conduct an exploratory study on the effects of the Mongolian medicine Saorilao-4 (SRL) on the gut microbiota structure, species abundance, and diversity of a rat PF model as well as the mechanisms underlying such effects.<br><br>METHODS AND RESULTS: Rat fecal samples were analyzed using 16S rRNA sequencing technology. Bioinformatic and correlation analyses were performed on microbiota data to determine significant associations. SRL substantially attenuated the adverse effects exerted by PF on the structure and diversity of gut microbiota while regulating its alpha and beta diversities. Linear discriminant analysis effect size enabled the identification of 62 differentially abundant microbial taxa. Gut microbiota abundance analysis revealed that SRL significantly increased the relative abundance of bacterial phyla such as Firmicutes and Bacteroidetes. Moreover, SRL increased the proportion of beneficial bacteria, such as Lactobacillus and Bifidobacteriales, decreased the proportion of pathogenic bacteria, such as Rikenellaceae, and balanced the gut microbiota by regulating metabolic pathways.<br><br>CONCLUSIONS: SRL may attenuate PF by regulating gut microbiota. This exploratory study establishes the groundwork for investigating the metagenomics of PF.},
}
@article {pmid38980075,
year = {2024},
author = {Feng, Z and Zhu, J and Zhang, L and Li, C and Su, D and Wang, H and Yu, Y and Song, L},
title = {Microbiological and functional traits of peri-implant mucositis and correlation with disease severity.},
journal = {mSphere},
volume = {9},
number = {7},
pages = {e0005924},
doi = {10.1128/msphere.00059-24},
pmid = {38980075},
issn = {2379-5042},
support = {82170990, 81870793//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020MZYS08//high-level professional physician training program of Minhang District/ ; },
mesh = {Humans ; Male ; Middle Aged ; Female ; *Bacteria/classification/isolation &amp; purification/genetics ; *Dental Implants/microbiology/adverse effects ; *Microbiota ; Adult ; *Dysbiosis/microbiology ; Severity of Illness Index ; Aged ; Gingivitis/microbiology ; Peri-Implantitis/microbiology ; Mucositis/microbiology ; Stomatitis/microbiology/etiology ; Metagenome ; Biofilms/growth &amp; development ; },
abstract = {Osseointegrated dental implants replace missing teeth and create an artificial surface for biofilms of complex microbial communities to grow. These biofilms on implants and dental surfaces can trigger infection and inflammation in the surrounding tissue. This study investigated the microbial characteristics of peri-implant mucositis (PM) and explored the correlation between microbial ecological imbalance, community function, and disease severity by comparing the submucosal microflora from PM with those of healthy inter-subject implants and intra-subject gingivitis (G) within a group of 32 individuals. We analyzed submucosal plaques from PM, healthy implant (HI), and G sites using metagenome shotgun sequencing. The bacterial diversity of HIs was higher than that of PM, according to the Simpson index. Beta diversity revealed differences in taxonomic and functional compositions across the groups. Linear discriminant analysis of the effect size identified 15 genera and 37 species as biomarkers that distinguished PM from HIs. Pathways involving cell motility and protein processing in the endoplasmic reticulum were upregulated in PM, while pathways related to the metabolism of cofactors and vitamins were downregulated. Microbial dysbiosis correlated positively with the severity of clinical inflammation measured by the sulcus bleeding index (SBI) in PM. Prevotella and protein processing in the endoplasmic reticulum also correlated positively with the SBI. Our study revealed PM's microbiological and functional traits and suggested the importance of certain functions in disease severity.IMPORTANCEPeri-implant mucositis is an early stage in the progression of peri-implantitis. The high prevalence of it has been a threat to the widespread use of implant prosthodontics. The link between the submucosal microbiome and peri-implant mucositis was demonstrated previously. Nevertheless, the taxonomic and functional composition of the peri-implant mucositis microbiome remains controversial. In this study, we comprehensively characterize the microbial signature of peri-implant mucositis and for the first time, we investigate the correlations between microbial dysbiosis, functional potential, and disease severity. With the help of metagenomic sequencing, we find the positive correlations between microbial dysbiosis, genus Prevotella, pathway of protein processing in the endoplasmic reticulum, and more severe mucosal bleeding in the peri-implant mucositis. Our studies offer insight into the pathogenesis of peri-implant mucositis by providing information on the relationships between community function and disease severity.},
}
@article {pmid38860762,
year = {2024},
author = {Li, Y and Xue, Y and Roy Chowdhury, T and Graham, DE and Tringe, SG and Jansson, JK and Taş, N},
title = {Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.},
journal = {mSphere},
volume = {9},
number = {7},
pages = {e0025924},
doi = {10.1128/msphere.00259-24},
pmid = {38860762},
issn = {2379-5042},
support = {NGEE Arctic//U.S. Department of Energy (DOE)/ ; DE-AC0205CH11231//U.S. Department of Energy (DOE)/ ; 41871067//MOST | National Natural Science Foundation of China (NSFC)/ ; //China Scholarship Council (CSC)/ ; //U.S. Department of Energy (DOE)/ ; DE-AC06-76RL01830//DOE | SC | Pacific Northwest National Laboratory (PNNL)/ ; },
mesh = {*Permafrost/microbiology ; *Soil Microbiology ; Arctic Regions ; *Carbon/metabolism ; *Oxidation-Reduction ; *Soil/chemistry ; *Microbiota ; Climate Change ; Bacteria/genetics/metabolism/classification ; Metagenome ; Methane/metabolism ; Freezing ; },
abstract = {UNLABELLED: Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.<br><br>IMPORTANCE: As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.},
}
@article {pmid38832716,
year = {2024},
author = {Hallberg, ZF and Nicolas, AM and Alvarez-Aponte, ZI and Mok, KC and Sieradzki, ET and Pett-Ridge, J and Banfield, JF and Carlson, HK and Firestone, MK and Taga, ME},
title = {Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae094},
pmid = {38832716},
issn = {1751-7370},
support = {//U.S. Department of Energy/ ; //Office of Science/ ; //Office of Biological and Environmental Research/ ; DE-SC0020155//Genomic Science Program/ ; 5K99GM143653-02/NH/NIH HHS/United States ; //DOE/ ; //Office of Biological and Environmental Research/ ; SCW1632//Genomic Science Program LLNL "Microbes Persist" Scientific Focus Area/ ; },
mesh = {*Soil Microbiology ; *Corrinoids/metabolism ; *Vitamin B 12/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Archaea/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Metagenome ; Soil/chemistry ; Grassland ; },
abstract = {Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.},
}
@article {pmid39073596,
year = {2024},
author = {Shah, RR and Larrondo, J and Dawson, T and Mcmichael, A},
title = {Scalp microbiome: a guide to better understanding scalp diseases and treatments.},
journal = {Archives of dermatological research},
volume = {316},
number = {8},
pages = {495},
pmid = {39073596},
issn = {1432-069X},
support = {H17/01/a0/004//Agency for Science, Technology and Research/ ; },
mesh = {Humans ; *Microbiota/drug effects/immunology ; *Scalp/microbiology ; Scalp Dermatoses/microbiology/drug therapy/therapy ; Dysbiosis/microbiology/immunology ; Folliculitis/microbiology/diagnosis/drug therapy/therapy ; Psoriasis/microbiology/drug therapy/immunology/therapy ; Dermatitis, Seborrheic/microbiology/drug therapy/therapy ; Alopecia Areata/microbiology/immunology/therapy/drug therapy ; Dandruff/microbiology/drug therapy ; },
abstract = {The scalp microbiome represents an array of microorganisms important in maintaining scalp homeostasis and mediating inflammation. Scalp microbial dysregulation has been implicated in dermatologic conditions including alopecia areata (AA), dandruff/seborrheic dermatitis (D/SD), scalp psoriasis (SP) and folliculitis decalvans (FD). Understanding the impact of scalp microbial dysbiosis gives insight on disease pathophysiology and guides therapeutic decision making. Herein we review the scalp microbiome and its functional role in scalp conditions by analysis of metagenomic medical literature in alopecia, D/SD, SP, and other dermatologic disease.Increased abundance of Malassezia, Staphylococcus, and Brevibacterium was associated with SD compared to healthy controls. A higher proportion of Corynebacterium, actinobacteria, and firmicutes are present in AA patients, and lower proportions of Staphylococcus caprae are associated with worse clinical outcomes. Decreased prevalence of actinobacteria and Propionibacterium and increased firmicutes, staphylococcus, and streptococcus are associated with scalp psoriasis. Studies of central centrifugal cicatricial alopecia (CCCA) suggest scalp microbial composition contributes to CCCA's pro-inflammatory status. The most common organisms associated with FD include methicillin-resistant S. aureus and S. lugdunensis. Antifungals have been a mainstay treatment for these diseases, while other alternatives including coconut oils and shampoos with heat-killed probiotics have shown considerable potential efficacy by replenishing the scalp microbiome.},
}
@article {pmid39069899,
year = {2024},
author = {Ambat, A and Antony, L and Maji, A and Ghimire, S and Mattiello, S and Kashyap, PC and More, S and Sebastian, V and Scaria, J},
title = {Enhancing recovery from gut microbiome dysbiosis and alleviating DSS-induced colitis in mice with a consortium of rare short-chain fatty acid-producing bacteria.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2382324},
doi = {10.1080/19490976.2024.2382324},
pmid = {39069899},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Humans ; *Dysbiosis/microbiology ; Mice ; *Dextran Sulfate ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Colitis/microbiology/chemically induced ; Disease Models, Animal ; Mice, Inbred C57BL ; Microbial Consortia ; Male ; Female ; Colitis, Ulcerative/microbiology/metabolism ; Germ-Free Life ; },
abstract = {The human gut microbiota is a complex community comprising hundreds of species, with a few present in high abundance and the vast majority in low abundance. The biological functions and effects of these low-abundant species on their hosts are not yet fully understood. In this study, we assembled a bacterial consortium (SC-4) consisting of B. paravirosa, C. comes, M. indica, and A. butyriciproducens, which are low-abundant, short-chain fatty acid (SCFA)-producing bacteria isolated from healthy human gut, and tested its effect on host health using germ-free and human microbiota-associated colitis mouse models. The selection also favored these four bacteria being reduced in abundance in either Ulcerative Colitis (UC) or Crohn's disease (CD) metagenome samples. Our findings demonstrate that SC-4 can colonize germ-free (GF) mice, increasing mucin thickness by activating MUC-1 and MUC-2 genes, thereby protecting GF mice from Dextran Sodium Sulfate (DSS)-induced colitis. Moreover, SC-4 aided in the recovery of human microbiota-associated mice from DSS-induced colitis, and intriguingly, its administration enhanced the alpha diversity of the gut microbiome, shifting the community composition closer to control levels. The results showed enhanced phenotypes across all measures when the mice were supplemented with inulin as a dietary fiber source alongside SC-4 administration. We also showed a functional redundancy existing in the gut microbiome, resulting in the low abundant SCFA producers acting as a form of insurance, which in turn accelerates recovery from the dysbiotic state upon the administration of SC-4. SC-4 colonization also upregulated iNOS gene expression, further supporting its ability to produce an increasing number of goblet cells. Collectively, our results provide evidence that low-abundant SCFA-producing species in the gut may offer a novel therapeutic approach to IBD.},
}
@article {pmid38989659,
year = {2024},
author = {Zhou, L and Yan, Z and Yang, S and Lu, G and Nie, Y and Ren, Y and Xue, Y and Shi, JS and Xu, ZH and Geng, Y},
title = {High methionine intake alters gut microbiota and lipid profile and leads to liver steatosis in mice.},
journal = {Food &amp; function},
volume = {15},
number = {15},
pages = {8053-8069},
doi = {10.1039/d4fo01613k},
pmid = {38989659},
issn = {2042-650X},
mesh = {Animals ; *Methionine/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Mice, Inbred C57BL ; *Liver/metabolism ; Fatty Liver/metabolism ; Lipid Metabolism/drug effects ; Lipids ; },
abstract = {Methionine is an important sulfur-containing amino acid. Health effects of both methionine restriction (MR) and methionine supplementation (MS) have been studied. This study aimed to investigate the impact of a high-methionine diet (HMD) (1.64% methionine) on both the gut and liver functions in mice through multi-omic analyses. Hepatic steatosis and compromised gut barrier function were observed in mice fed the HMD. RNA-sequencing (RNA-seq) analysis of liver gene expression patterns revealed the upregulation of lipid synthesis and degradation pathways, cholesterol metabolism and inflammation-related nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Metagenomic sequencing of cecal content demonstrated a shift in gut microbial composition with an increased abundance of opportunistic pathogens and gut microbial functions with up-regulated lipopolysaccharide (LPS) biosynthesis in mice fed HMD. Metabolomic study of cecal content showed an altered gut lipid profile and the level of bioactive lipids, including docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), palmitoylethanolamide (PEA), linoleoyl ethanolamide (LEA) and arachidonoyl ethanolamide (AEA), that carry anti-inflammatory effects significantly reduced in the gut of mice fed the HMD. Correlation analysis demonstrated that gut microbiota was highly associated with liver and gut functions and gut bioactive lipid content. In conclusion, this study suggested that the HMD exerted negative impacts on both the gut and liver, and an adequate amount of methionine intake should be carefully determined to ensure normal physiological function without causing adverse effects.},
}
@article {pmid39068184,
year = {2024},
author = {de Jonge, PA and van den Born, BH and Zwinderman, AH and Nieuwdorp, M and Dutilh, BE and Herrema, H},
title = {Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6346},
pmid = {39068184},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 0915018201002//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 015.017.050//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2019.82.004//Diabetes Fonds (Dutch Diabetes Research Foundation)/ ; },
mesh = {Humans ; *Phylogeny ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Gastrointestinal Microbiome/genetics ; Genome, Viral/genetics ; Metagenome/genetics ; Virome/genetics ; Inflammatory Bowel Diseases/virology ; Biodiversity ; Diabetes Mellitus, Type 2/virology ; Female ; Male ; Europe ; Netherlands ; Adult ; },
abstract = {Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.},
}
@article {pmid39068001,
year = {2024},
author = {Li, Y and Han, S},
title = {Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases.},
journal = {Gastroenterology clinics of North America},
volume = {53},
number = {3},
pages = {383-397},
doi = {10.1016/j.gtc.2023.12.008},
pmid = {39068001},
issn = {1558-1942},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Host Microbial Interactions ; Biomarkers/metabolism ; Precision Medicine ; },
abstract = {The human gut microbiota, consisting of trillions of microorganisms, encodes diverse metabolic pathways that impact numerous aspects of host physiology. One key way in which gut bacteria interact with the host is through the production of small metabolites. Several of these microbiota-dependent metabolites, such as short-chain fatty acids, have been shown to modulate host diseases. In this review, we examine how disease-associated metabolic signatures are identified using metabolomic platforms, and where metabolomics is applied in gut microbiota-disease interactions. We further explore how integration of metagenomic and metabolomic data in human studies can facilitate biomarkers discoveries in precision medicine.},
}
@article {pmid39066857,
year = {2024},
author = {de Matos, JP and Ribeiro, DF and da Silva, AK and de Paula, CH and Cordeiro, IF and Lemes, CGC and Sanchez, AB and Rocha, LCM and Garcia, CCM and Almeida, NF and Alves, RM and de Abreu, VAC and Varani, AM and Moreira, LM},
title = {Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {73},
pmid = {39066857},
issn = {1617-4623},
support = {#2019/25176-0//FAPESP/ ; 075/2020//FAPESPA/ ; 306039/2021-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304367/2022-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-02357-17//FAPEMIG/ ; },
mesh = {*Plant Leaves/microbiology/genetics ; *Plant Diseases/microbiology/genetics ; Disease Resistance/genetics ; Microbiota/genetics ; Ecosystem ; Actinobacteria/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome/genetics ; Phylogeny ; Brassicaceae/microbiology/genetics ; },
abstract = {Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.},
}
@article {pmid39066334,
year = {2024},
author = {Mbigha Donfack, KC and De Coninck, L and Ghogomu, SM and Matthijnssens, J},
title = {Aedes Mosquito Virome in Southwestern Cameroon: Lack of Core Virome, But a Very Rich and Diverse Virome in Ae. africanus Compared to Other Aedes Species.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066334},
issn = {1999-4915},
support = {BE2022GMUKULA101//Vlaamse Interuniversitaire Raad/ ; C14/20/108//KU Leuven/ ; 11L1323N//Research Foundation Flanders (FWO)/ ; },
mesh = {Animals ; *Aedes/virology ; Cameroon ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; Genome, Viral ; Arboviruses/genetics/classification/isolation &amp; purification ; },
abstract = {In Cameroon, Aedes mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the Aedes virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 Aedes mosquitoes were collected from four locations (Bafoussam, Buea, Edea, and Yaounde). Aedes albopictus dominated all sites except for Bafoussam, where Aedes africanus prevailed. Metagenomic analyses of the mosquitoes grouped per species into 54 pools revealed notable differences in the eukaryotic viromes between Ae. africanus and Ae. albopictus, with the former exhibiting greater richness and diversity. Thirty-seven eukaryotic virus species from 16 families were identified, including six novel viruses with near complete genome sequences. Seven viruses were further quantified in individual mosquitoes via qRT-PCR. Although none of them could be identified as core viruses, Guangzhou sobemo-like virus and Bafoussam mosquito solemovirus, were highly prevalent regionally in Ae. albopictus and Ae. africanus, respectively. This study highlights the diverse eukaryotic virome of Aedes species in southwestern Cameroon. Despite their shared genus, Aedes species exhibit limited viral sharing, with varying viral abundance and prevalence across locations. Ae. africanus, an understudied vector, harbors a rich and diverse virome, suggesting potential implications for arbovirus vector competence.},
}
@article {pmid39066322,
year = {2024},
author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Adame-Gallegos, JR and De Luna Santillana, EJ and Huerta, H and Gonzalez-Peña, R and Rivera-Martínez, A and Rubio-Tabares, E and Beristain-Ruiz, DM and Blitvich, BJ},
title = {Discovery of Novel Viruses in Culicoides Biting Midges in Chihuahua, Mexico.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066322},
issn = {1999-4915},
mesh = {Animals ; *Ceratopogonidae/virology ; Mexico ; *Phylogeny ; Female ; Metagenomics ; Virome ; High-Throughput Nucleotide Sequencing ; Insect Vectors/virology ; Genome, Viral ; },
abstract = {Biting midges (Culicoides) are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in Culicoides from Mexico. A total of 457 adult midges were collected in Chihuahua, northern Mexico, in 2020 and 2021, and all were identified as female Culicoides reevesi. The midges were sorted into five pools and homogenized. An aliquot of each homogenate was subjected to polyethylene glycol precipitation to enrich for virions, then total RNA was extracted and analyzed by unbiased high-throughput sequencing. We identified six novel viruses that are characteristic of viruses from five families (Nodaviridae, Partitiviridae, Solemoviridae, Tombusviridae, and Totiviridae) and one novel virus that is too divergent from all classified viruses to be assigned to an established family. The newly discovered viruses are phylogenetically distinct from their closest known relatives, and their minimal infection rates in female C. reevesi range from 0.22 to 1.09. No previously known viruses were detected, presumably because viral metagenomics had never before been used to study Culicoides from the Western Hemisphere. To conclude, we discovered multiple novel viruses in C. reevesi from Mexico, expanding our knowledge of arthropod viral diversity and evolution.},
}
@article {pmid39066262,
year = {2024},
author = {Paietta, EN and Kraberger, S and Lund, MC and Vargas, KL and Custer, JM and Ehmke, E and Yoder, AD and Varsani, A},
title = {Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066262},
issn = {1999-4915},
support = {internal//TriCEM (Triangle Center for Evolutionary Medicine), Duke Biology, Duke Lemur Center, Duke University/ ; },
mesh = {Animals ; *Feces/virology ; *Lemur/virology ; *Genome, Viral ; Phylogeny ; Virome ; DNA, Viral/genetics ; Mouth/virology ; Madagascar ; Blood/virology ; },
abstract = {Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.},
}
@article {pmid39066231,
year = {2024},
author = {Liu, D and Zhang, Z and Wang, Z and Xue, L and Liu, F and Lu, Y and Yu, S and Li, S and Zheng, H and Zhang, Z and Tian, Z},
title = {Transposase-Assisted RNA/DNA Hybrid Co-Tagmentation for Target Meta-Virome of Foodborne Viruses.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066231},
issn = {1999-4915},
support = {2022YFC2302800//National Key Research and Development Program of China/ ; 2022M722152//China Postdoctoral Science Foundation/ ; 23YF1440400//Shanghai Rising-Star Program/ ; SKLAM007-2022//State Key Laboratory of Applied Microbiology Southern China/ ; RC2024-02//Innovation Promotion Program of NHC and Shanghai Key Labs SIBPT/ ; 2022HK136//General Administration of Customs Project/ ; },
mesh = {*Transposases/genetics/metabolism ; *Genome, Viral ; *Foodborne Diseases/virology ; Humans ; *Metagenomics/methods ; Virome/genetics ; RNA, Viral/genetics ; Norovirus/genetics/classification ; Gene Library ; DNA, Viral/genetics ; Viruses/genetics/classification ; },
abstract = {Foodborne diseases are major public health problems globally. Metagenomics has emerged as a widely used tool for pathogen screening. In this study, we conducted an updated Tn5 transposase-assisted RNA/DNA hybrid co-tagmentation (TRACE) library construction approach. To address the detection of prevalent known foodborne viruses and the discovery of unknown pathogens, we employed both specific primers and oligo-T primers during reverse transcription. The method was validated using clinical samples confirmed by RT-qPCR and compared with standard RNA-seq library construction methods. The mapping-based approach enabled the retrieval of nearly complete genomes (>95%) for the majority of virus genome segments (86 out of 88, 97.73%), with a mean coverage depth of 21,494.53× (ranging from 77.94× to 55,688.58×). Co-infection phenomena involving prevalent genotypes of Norovirus with Astrovirus and Human betaherpesvirus 6B were observed in two samples. The updated TRACE-seq exhibited superior performance in viral reads percentages compared to standard RNA-seq library preparation methods. This updated method has expanded its target pathogens beyond solely Norovirus to include other prevalent foodborne viruses. The feasibility and potential effectiveness of this approach were then evaluated as an alternative method for surveilling foodborne viruses, thus paving the way for further exploration into whole-genome sequencing of viruses.},
}
@article {pmid39066202,
year = {2024},
author = {McDonnell, B and Parlindungan, E and Vasiliauskaite, E and Bottacini, F and Coughlan, K and Krishnaswami, LP and Sassen, T and Lugli, GA and Ventura, M and Mastroleo, F and Mahony, J and van Sinderen, D},
title = {Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066202},
issn = {1999-4915},
support = {15/SIRG/3430/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; MELiSSA POMP//European Space Agency/ ; },
mesh = {*Fermentation ; *Metagenomics/methods ; *Spirulina/genetics ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Biodiversity ; Metagenome ; Virome ; Phylogeny ; Ponds/microbiology/virology ; Bacteria/virology/genetics/classification/isolation &amp; purification ; },
abstract = {Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations.},
}
@article {pmid39066183,
year = {2024},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {Diversity of Picorna-Like Viruses in the Teltow Canal, Berlin, Germany.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066183},
issn = {1999-4915},
mesh = {*Genome, Viral ; *Phylogeny ; *Picornaviridae/genetics/classification/isolation &amp; purification ; Berlin ; Fresh Water/virology ; Virome/genetics ; RNA, Viral/genetics ; Germany ; Genetic Variation ; RNA Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {The viromes of freshwater bodies are underexplored. The Picornavirales order, with 371 acknowledged species, is one of the most expansive and diverse groups of eukaryotic RNA viruses. In this study, we add 513 picorna-like viruses to the assemblage of more than 2000 unassigned picorna-like viruses. Our set of the aquatic Picornavirales virome of the Teltow Canal in Berlin, Germany, consists of 239 complete and 274 partial genomes. This urban freshwater body is characterized by the predominance of marna-like viruses (30.8%) and dicistro-like viruses (19.1%), whereas picornaviruses, iflaviruses, solinvi-like viruses, polycipi-like viruses, and nora-like viruses are considerably less prevalent. Caliciviruses and secoviruses were absent in our sample. Although presenting characteristic domains of Picornavirales, more than 100 viruses (20.8%) could not be assigned to any of the 9 Picornavirales families. Thirty-three viruses of the Marnaviridae-mostly locarna-like viruses-exhibit a monocistronic genome layout. Besides a wealth of novel virus sequences, viruses with peculiar features are reported. Among these is a clade of untypeable marna-like viruses with dicistronic genomes, but with the capsid protein-encoding open reading frame located at the 5' part of their RNA. A virus with a similar genome layout but clustering with dicistroviruses was also observed. We further detected monocistronic viruses with a polymerase gene related to aparaviruses. The detection of Aichi virus and five novel posa-like viruses indicates a slight burden in municipal wastewater.},
}
@article {pmid39064618,
year = {2024},
author = {Tsifintaris, M and Sitmalidis, M and Tokamani, M and Anastasiadi, C and Georganta, M and Tsochantaridis, I and Vlachakis, D and Tsikouras, P and Nikolettos, N and Chrousos, GP and Sandaltzopoulos, R and Giannakakis, A},
title = {Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals.},
journal = {Nutrients},
volume = {16},
number = {14},
pages = {},
pmid = {39064618},
issn = {2072-6643},
support = {05704//Hellenic Foundation for Research and Innovation/ ; },
mesh = {Animals ; Humans ; *Milk, Human/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; Greece ; *Microbiota ; Female ; Cattle ; *Goats ; *Colostrum/microbiology ; *Milk/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Milk is a biological fluid with a dynamic composition of micronutrients and bioactive molecules that serves as a vital nutrient source for infants. Milk composition is affected by multiple factors, including genetics, geographical location, environmental conditions, lactation phase, and maternal nutrition, and plays a key role in dictating its microbiome. This study addresses a less-explored aspect, comparing the microbial communities in human breast milk with those in mature milk from species that are used for milk consumption. Since mature animal milk is used as a supplement for both the infant (formula) and the child/adolescent, our main aim was to identify shared microbial communities in colostrum and mature human milk. Using 16S rRNA metagenomic sequencing, we focused on characterizing the milk microbiota in the Northern Greek population by identifying shared microbial communities across samples and comparing the relative abundance of prevalent genera. We analyzed ten human milk samples (from five mothers), with five collected three days postpartum (colostrum) and five collected thirty to forty days postpartum (mature milk) from corresponding mothers. To perform an interspecies comparison of human milk microbiota, we analyzed five goat and five bovine milk samples from a local dairy industry, collected fifty to seventy days after birth. Alpha diversity analysis indicated moderate diversity and stability in bovine milk, high richness in goat milk, and constrained diversity in breast milk. Beta diversity analysis revealed significant distinctions among mammalian species, emphasizing both presence/absence and abundance-based clustering. Despite noticeable differences, shared microbial components underscore fundamental aspects across all mammalian species, highlighting the presence of a core microbiota predominantly comprising the Proteobacteria, Firmicutes, and Actinobacteriota phyla. At the genus level, Acinetobacter, Gemella, and Sphingobium exhibit significant higher abundance in human milk compared to bovine and goat milk, while Pseudomonas and Atopostipes are more prevalent in animal milk. Our comparative analysis revealed differences and commonalities in the microbial communities of various mammalian milks and unraveled the existence of a common fundamental milk core microbiome. We thus revealed both species-specific and conserved microbial communities in human, bovine, and goat milk. The existence of a common core microbiome with conserved differences between colostrum and mature human milk underscores fundamental similarities in the microbiota of milk across mammalian species, which could offer valuable implications for optimizing the nutritional quality and safety of dairy products as well as supplements for infant health.},
}
@article {pmid39063072,
year = {2024},
author = {Zhang, T and Yue, Y and Li, C and Wu, X and Park, S},
title = {Vagus Nerve Suppression in Ischemic Stroke by Carotid Artery Occlusion: Implications for Metabolic Regulation, Cognitive Function, and Gut Microbiome in a Gerbil Model.},
journal = {International journal of molecular sciences},
volume = {25},
number = {14},
pages = {},
pmid = {39063072},
issn = {1422-0067},
support = {RS-2023-00208567//National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Vagus Nerve/metabolism ; *Gerbillinae ; *Disease Models, Animal ; *Cognition ; Male ; Ischemic Stroke/metabolism ; Diet, High-Fat/adverse effects ; Brain-Gut Axis/physiology ; Vagotomy ; Hippocampus/metabolism ; Brain-Derived Neurotrophic Factor/metabolism ; },
abstract = {The vagus nerve regulates metabolic homeostasis and mediates gut-brain communication. We hypothesized that vagus nerve dysfunction, induced by truncated vagotomy (VGX) or carotid artery occlusion (AO), would disrupt gut-brain communication and exacerbate metabolic dysregulation, neuroinflammation, and cognitive impairment. This study aimed to test the hypothesis in gerbils fed a high-fat diet. The gerbils were divided into four groups: AO with VGX (AO_VGX), AO without VGX (AO_NVGX), no AO with VGX (NAO_VGX), and no AO without VGX (NAO_NVGX). After 5 weeks on a high-fat diet, the neuronal cell death, neurological severity, hippocampal lipids and inflammation, energy/glucose metabolism, intestinal morphology, and fecal microbiome composition were assessed. AO and VGX increased the neuronal cell death and neurological severity scores associated with increased hippocampal lipid profiles and lipid peroxidation, as well as changes in the inflammatory cytokine expression and brain-derived neurotrophic factor (BDNF) levels. AO and VGX also increased the body weight, visceral fat mass, and insulin resistance and decreased the skeletal muscle mass. The intestinal morphology and microbiome composition were altered, with an increase in the abundance of Bifidobacterium and a decrease in Akkermansia and Ruminococcus. Microbial metagenome functions were also impacted, including glutamatergic synaptic activity, glycogen synthesis, and amino acid biosynthesis. Interestingly, the effects of VGX were not significantly additive with AO, suggesting that AO inhibited the vagus nerve activity, partly offsetting the effects of VGX. In conclusion, AO and VGX exacerbated the dysregulation of energy, glucose, and lipid metabolism, neuroinflammation, and memory deficits, potentially through the modulation of the gut-brain axis. Targeting the gut-brain axis by inhibiting vagus nerve suppression represents a potential therapeutic strategy for ischemic stroke.},
}
@article {pmid39062603,
year = {2024},
author = {Mosca, A and Dimaria, G and Nicotra, D and Modica, F and Massimino, ME and Catara, AF and Scuderi, G and Russo, M and Catara, V},
title = {Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062603},
issn = {2073-4425},
support = {08CT7211000254//PO FESR 2014-2020 Sicilia action 1.1.5/ ; },
mesh = {*Citrus/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Ascomycota/genetics/pathogenicity ; },
abstract = {Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.},
}
@article {pmid39060733,
year = {2024},
author = {Fasano, A and Matera, M},
title = {Probiotics to Prevent Celiac Disease and Inflammatory Bowel Diseases.},
journal = {Advances in experimental medicine and biology},
volume = {1449},
number = {},
pages = {95-111},
pmid = {39060733},
issn = {0065-2598},
mesh = {Humans ; *Celiac Disease/microbiology/genetics/prevention &amp; control ; *Inflammatory Bowel Diseases/microbiology/genetics/prevention &amp; control ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; },
abstract = {The incidence of chronic inflammatory diseases (CIDs) is dramatically increasing in the developed world, resulting in an increased burden of disease in childhood. Currently, there are limited effective strategies for treating or preventing these conditions. To date, myriads of cross-sectional studies have described alterations in the composition of the gut microbiota in a variety of disease states, after the disease has already occurred. We suggest that to mechanically link these microbiome changes with disease pathogenesis, a prospective cohort design is needed to capture changes that precede or coincide with disease onset and symptoms. In addition, these prospective studies must integrate microbiological, metagenomic, meta transcriptomic and metabolomic data with minimal and standardized clinical and environmental metadata that allow to correctly compare and interpret the results of the analysis of the human microbiota in order to build a system-level model of the interactions between the host and the development of the disease. The creation of new biological computational models thus constructed will allow us to finally move from the detection of simple elements of "association" to the identification of elements of real "causality" allowing to provide a mechanistic approach to the exploration of the development of CIDs.This can only be done when these diseases are studied as complex biological networks. In this chapter we discuss the current knowledge regarding the contribution of the microbiome to CID in childhood, focusing on celiac disease and inflammatory bowel disease, with the overall aim of identifying pathways to shift research from descriptive to mechanistic approaches. We then examine how some components of the microbiota, through epigenetic reprogramming, can start the march from genetic predisposition to clinical expression of CIDs, thus opening up new possibilities for intervention, through microbiota therapy targeting the manipulation of the composition and function of the microbiota, for future applications of precision medicine and primary prevention.},
}
@article {pmid39060557,
year = {2024},
author = {Hu, L and Wang, Z and Wang, Z and Wang, L and Fang, J and Liu, R},
title = {Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {282},
pmid = {39060557},
issn = {1432-0991},
support = {42276149//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Microbiota ; Archaea/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Seawater/microbiology ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Carbon/metabolism ; Biodiversity ; },
abstract = {The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.},
}
@article {pmid39060267,
year = {2024},
author = {Gao, JM and Xia, SY and Hide, G and Li, BH and Liu, YY and Wei, ZY and Zhuang, XJ and Yan, Q and Wang, Y and Yang, W and Chen, JH and Rao, JH},
title = {Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {61},
pmid = {39060267},
issn = {2055-5008},
support = {82200966//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31671311//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31671311//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Macaca fascicularis ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Disease Models, Animal ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Parkinsonian Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiota has been demonstrated to play a significant role in the pathogenesis of Parkinson's disease (PD). However, conflicting findings regarding specific microbial species have been reported, possibly due to confounding factors within human populations. Herein, our current study investigated the interaction between the gut microbiota and host in a non-human primate (NHP) PD model induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) using a multi-omic approach and a self-controlled design. Our transcriptomic sequencing of peripheral blood leukocytes (PBL) identified key genes involved in pro-inflammatory cytokine dysregulation, mitochondrial function regulation, neuroprotection activation, and neurogenesis associated with PD, such as IL1B, ATP1A3, and SLC5A3. The metabolomic profiles in serum and feces consistently exhibited significant alterations, particularly those closely associated with inflammation, mitochondrial dysfunctions and neurodegeneration in PD, such as TUDCA, ethylmalonic acid, and L-homophenylalanine. Furthermore, fecal metagenome analysis revealed gut dysbiosis associated with PD, characterized by a significant decrease in alpha diversity and altered commensals, particularly species such as Streptococcus, Butyrivibrio, and Clostridium. Additionally, significant correlations were observed between PD-associated microbes and metabolites, such as sphingomyelin and phospholipids. Importantly, PDPC significantly reduced in both PD monkey feces and serum, exhibiting strong correlation with PD-associated genes and microbes, such as SLC5A3 and Butyrivibrio species. Moreover, such multi-omic differential biomarkers were linked to the clinical rating scales of PD monkeys. Our findings provided novel insights into understanding the potential role of key metabolites in the host-microbiota interaction involved in PD pathogenesis.},
}
@article {pmid39059949,
year = {2024},
author = {Zhang, P and Wang, H and Klima, C and Yang, X},
title = {Microbiota in lymph nodes of cattle harvested in a Canadian meat processing plant.},
journal = {Food research international (Ottawa, Ont.)},
volume = {191},
number = {},
pages = {114693},
doi = {10.1016/j.foodres.2024.114693},
pmid = {39059949},
issn = {1873-7145},
mesh = {Animals ; Cattle ; Canada ; *Lymph Nodes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Abattoirs ; *Shiga-Toxigenic Escherichia coli/isolation &amp; purification/genetics ; *Microbiota ; *Salmonella/isolation &amp; purification/genetics/classification ; Red Meat/microbiology ; Food Microbiology ; },
abstract = {Lymph nodes (LN) harboring bacteria, when being incorporated into ground beef, may impact the microbial safety and quality of such products. We tested two main foodborne pathogens Salmonella and Shiga toxin-producing Escherichia coli (STEC) and profiled the microbiota in LNs (n = 160) of cattle harvested at a Canadian abattoir, by conventional plating methods, PCR, and high throughput sequencing. LNs at two anatomical locations, subiliac and popliteal from 80 cattle were included. All cattle had bacteria detected in popliteal and/or subiliac LNs with the maximum bacterial load of 5.4 and 2.8 log10CFU/g in popliteal and subiliac LNs, respectively. Neither Salmonella nor STEC was found in LNs although STEC was detected in a significant percentage of samples from beef hides (50.6 %) by plating and/or PCR. Both 16S rRNA gene amplicon and metagenome sequencing found the predominance of Escherichia (13-34.6 % among bacterial community), Clostridium (12.6-20.6 %) and Streptococcus (9.7-10 %) in popliteal LNs. Metagenomic sequencing was able to identify the predominant taxa at species level with E. coli (13 %), Clostridium perfringens (11.1 %) and Streptococcus uberis (6 %) predominant in LNs. Low prevalence/abundance of Salmonella was found by metagenomic sequencing. In conclusion, the relatively high bacterial load and diversity in LNs may affect the shelf life of ground beef and high relative abundance of E. coli would warrant further monitoring.},
}
@article {pmid38977060,
year = {2024},
author = {Liu, Q and Xu, Y and Lv, X and Guo, C and Zhu, H and Yang, L and Wang, Y},
title = {2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine alleviates diet-induced hyperlipidemia by modulating intestinal gene expression profiles and metabolic pathway.},
journal = {Life sciences},
volume = {352},
number = {},
pages = {122891},
doi = {10.1016/j.lfs.2024.122891},
pmid = {38977060},
issn = {1879-0631},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Cricetinae ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Hyperlipidemias/drug therapy/metabolism ; *Adenosine/metabolism ; Metabolic Networks and Pathways/drug effects ; Mesocricetus ; Intestines/drug effects/microbiology ; Transcriptome/drug effects ; },
abstract = {There is a growing body of evidence suggesting that the composition of intestinal flora plays a significant role in regulating lipid metabolism. 2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (IMMH007) is a new candidate compound for regulating blood cholesterol and other lipids. In this study, we conducted metagenomic and metabolomic analyses on samples from high-fat diet-fed (HFD) hamsters treated with IMMH007. Our findings revealed that IMM-H007 reversed the imbalance of gut microbiota caused by a high-fat diet. Additionally, it activated adiponectin receptor and pantothenate and CoA biosynthesis pathway-related genes, which are known to regulate lipid and glucose metabolism. Furthermore, IMM-H007 promotes cholesterol metabolism by reducing the abundance of genes and species associated with 7α-dehydroxylation and bile salt hydrolase (BSH). Metabolomics and pharmacological studies have shown that IMM-H007 effectively improved glucose and lipid metabolism disorders caused by HFD, reduced the aggregation of secondary bile acids (SBAs), significantly increased the content of hyodeoxycholic acid (HDCA), and also activated the expression of VDR in the small intestine. As a result, there was a reduction in the leakage of diamine oxidase (DAO) into the bloodstream in hamsters, accompanied by an upregulation of ZO-1 expression in the small intestine. The results suggested that IMM-H007 regulated glucose and lipid metabolism, promoted cholesterol metabolism through activating the expression of VDR, inhibiting inflammatory and improving the permeability of the intestinal barrier. Thus, our study provides new understanding of how IMM-H007 interacts with intestinal function, microbiota, and relevant targets, shedding light on its mechanism of action.},
}
@article {pmid38971433,
year = {2024},
author = {Favaron, A and Abdalla, Y and McCoubrey, LE and Nandiraju, LP and Shorthouse, D and Gaisford, S and Basit, AW and Orlu, M},
title = {Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {200},
number = {},
pages = {106845},
doi = {10.1016/j.ejps.2024.106845},
pmid = {38971433},
issn = {1879-0720},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Janus Kinase Inhibitors/pharmacology ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Sphingosine 1 Phosphate Receptor Modulators ; Pyrazoles/pharmacology ; Colon/microbiology/metabolism/drug effects ; Sulfonamides/pharmacology/administration &amp; dosage ; Purines ; Azetidines/pharmacology/administration &amp; dosage ; Benzyl Compounds/pharmacology/administration &amp; dosage ; Piperidines/pharmacology/administration &amp; dosage ; Pyrimidines/pharmacology/administration &amp; dosage ; Drug Delivery Systems/methods ; Oxadiazoles/pharmacology/administration &amp; dosage ; Sphingosine-1-Phosphate Receptors/metabolism/antagonists &amp; inhibitors ; Pyrroles/pharmacology/administration &amp; dosage ; Indans/pharmacology/administration &amp; dosage ; Pyridines ; Triazoles ; },
abstract = {The gut microbiota is a complex ecosystem, home to hundreds of bacterial species and a vast repository of enzymes capable of metabolising a wide range of pharmaceuticals. Several drugs have been shown to affect negatively the composition and function of the gut microbial ecosystem. Janus Kinase (JAK) inhibitors and Sphingosine-1-phosphate (S1P) receptor modulators are drugs recently approved for inflammatory bowel disease through an immediate release formulation and would potentially benefit from colonic targeted delivery to enhance the local drug concentration at the diseased site. However, their impact on the human gut microbiota and susceptibility to bacterial metabolism remain unexplored. With the use of calorimetric, optical density measurements, and metagenomics next-generation sequencing, we show that JAK inhibitors (tofacitinib citrate, baricitinib, filgotinib) have a minor impact on the composition of the human gut microbiota, while ozanimod exerts a significant antimicrobial effect, leading to a prevalence of the Enterococcus genus and a markedly different metabolic landscape when compared to the untreated microbiota. Moreover, ozanimod, unlike the JAK inhibitors, is the only drug subject to enzymatic degradation by the human gut microbiota sourced from six healthy donors. Overall, given the crucial role of the gut microbiome in health, screening assays to investigate the interaction of drugs with the microbiota should be encouraged for the pharmaceutical industry as a standard in the drug discovery and development process.},
}
@article {pmid38968070,
year = {2024},
author = {Shridhar, SV and Beghini, F and Alexander, M and Singh, A and Juárez, RM and Brito, IL and Christakis, NA},
title = {Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages.},
journal = {Cell reports},
volume = {43},
number = {7},
pages = {114442},
doi = {10.1016/j.celrep.2024.114442},
pmid = {38968070},
issn = {2211-1247},
mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Socioeconomic Factors ; Female ; Male ; Adult ; Bacteria/classification/genetics ; Phylogeny ; Middle Aged ; },
abstract = {Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.},
}
@article {pmid38960872,
year = {2024},
author = {Lee, H and Park, W and No, J and Hyung, NW and Lee, JY and Kim, S and Yang, H and Lee, P and Kim, E and Oh, KB and Yoo, JG and Lee, S},
title = {Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF Pigs.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {7},
pages = {1484-1490},
doi = {10.4014/jmb.2402.02018},
pmid = {38960872},
issn = {1738-8872},
mesh = {Animals ; *Gastrointestinal Microbiome ; Swine/microbiology ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Metagenome ; Adaptation, Physiological ; },
abstract = {The gut microbiota is a key factor significantly impacting host health by influencing metabolism and immune function. Its composition can be altered by genetic factors, as well as environmental factors such as the host's surroundings, diet, and antibiotic usage. This study aims to examine how the characteristics of the gut microbiota in pigs, used as source animals for xenotransplantation, vary depending on their rearing environment. We compared the diversity and composition of gut microbiota in fecal samples from pigs raised in specific pathogen-free (SPF) and conventional (non-SPF) facilities. The 16S RNA metagenome sequencing results revealed that pigs raised in non-SPF facilities exhibited greater gut microbiota diversity compared to those in SPF facilities. Genera such as Streptococcus and Ruminococcus were more abundant in SPF pigs compared to non-SPF pigs, while Blautia, Bacteroides, and Roseburia were only observed in SPF pigs. Conversely, Prevotella was exclusively present in non-SPF pigs. It was predicted that SPF pigs would show higher levels of processes related to carbohydrate and nucleotide metabolism, and environmental information processing. On the other hand, energy and lipid metabolism, as well as processes associated with genetic information, cell communication, and diseases, were predicted to be more active in the gut microbiota of non-SPF pigs. This study provides insights into how the presence or absence of microorganisms, including pathogens, in pig-rearing facilities affects the composition and function of the pigs' gut microbiota. Furthermore, this serves as a reference for tracing whether xenotransplantation source pigs were maintained in a pathogen-controlled environment.},
}
@article {pmid38959851,
year = {2024},
author = {Hoetzinger, M and Hahn, MW and Andersson, LY and Buckley, N and Ramsin, C and Buck, M and Nuy, JK and Garcia, SL and Puente-Sánchez, F and Bertilsson, S},
title = {Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae113},
pmid = {38959851},
issn = {1751-7370},
support = {2017-04422//Swedish Research Council/ ; 2019-02336//Swedish Research Council Formas/ ; UNI-0404/2370//Tiroler Wissenschaftsf&#xf6;rderung/ ; 27160-B22//Austrian Science Fund/ ; 300846//Research Council of Norway/ ; 311913//ERA-Net Cofund Project BlueBio/ ; 892961//European Union's Horizon 2020/ ; 2022-04801//Swedish Research Council/ ; },
mesh = {*Fresh Water/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Phylogeny ; Population Dynamics ; Ecosystem ; Biodiversity ; Genome, Bacterial ; Phylogeography ; },
abstract = {Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available and new freshwater metagenomes in combination with the genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated with the predominant freshwater taxa acI, LD12, Polynucleobacter, and Candidatus Methylopumilus. Despite the broad geographic ranges, each species appeared as a sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on a global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. The change in an LD12 population over 7 years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely 2 months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures, we propose distinct models of speciation.},
}
@article {pmid38959642,
year = {2024},
author = {Cao, G and Yu, Y and Wang, H and Yang, H and Tao, F and Yang, S and Liu, J and Li, Z and Yang, C},
title = {Dietary Clostridium butyricum and 25-Hydroxyvitamin D3 modulate bone metabolism of broilers through the gut-brain axis.},
journal = {Poultry science},
volume = {103},
number = {8},
pages = {103966},
pmid = {38959642},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology ; *Clostridium butyricum/physiology ; *Animal Feed/analysis ; *Diet/veterinary ; *Calcifediol/administration &amp; dosage/pharmacology ; *Dietary Supplements/analysis ; Brain-Gut Axis/physiology/drug effects ; Probiotics/pharmacology/administration &amp; dosage ; Male ; Bone and Bones/drug effects ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Leg disorders have become increasingly common in broilers, leading to lower meat quality and major economic losses. This study evaluated the effects of dietary supplementation with Clostridium butyricum (C. butyricum) and 25-hydroxyvitamin D3 (25-OH-D3) on bone development by comparing growth performance, tibial parameters, Ca and P contents of tibial ash, bone development-related indicators' level, and cecal short-chain fatty acids in Cobb broilers. All birds were divided into four treatment groups, which birds fed either a basal diet (Con), basal diet + 75 mg chlortetracycline/kg (Anti), basal diet + C. butyricum at 10[9] CFU/kg (Cb), basal diet + C. butyricum at 10[9] CFU/kg and 25-OH-D3 at 25 μg/kg (CbD), or basal diet + 25-OH-D3 at 25 μg/kg (CD). Our results suggest that the dietary supplementation in Cb, CbD, and CD significantly increased the body weight (BW) and average daily gain (ADG), and reduced the feed-to-weight ratio (F/G) at different stages of growth (P < 0.05). Dietary supplementation in Cb, CbD, and CD prolonged (P < 0.05) the behavioral responses latency-to-lie (LTL) time, reduced (P < 0.05) the levels of osteocalcin (BGP) and peptide tyrosine (PYY), and increased (P < 0.05) serotonin (5-HT) and dopamine (DA). Treatment with Cb increased (P < 0.05) the levels of acetic acid, isobutyric acid, butyric acid, and isovaleric acid compared with those in Con group. The cecal metagenome showed that Alistipes spp. were significantly more abundant in Cb, CbD, and CD groups (P < 0.05). A total of 12 metabolic pathways were significantly affected by supplementation, including the signaling pathways of glucagon, insulin, and PI3K-AKT; primary and secondary bile acid biosynthesis; and P-type Ca 2+ transporters (P < 0.05). Hence, the CbD supplementation modulates bone metabolism by regulating the mediators of gut-brain axis, which may inform strategies to prevent leg diseases and improve meat quality in broilers.},
}
@article {pmid38870614,
year = {2024},
author = {Xiong, X and Lan, Y and Wang, Z and Xu, J and Gong, J and Chai, X},
title = {Bacteroidales reduces growth rate through serum metabolites and cytokines in Chinese Ningdu yellow chickens.},
journal = {Poultry science},
volume = {103},
number = {8},
pages = {103905},
pmid = {38870614},
issn = {1525-3171},
mesh = {Animals ; *Chickens/growth &amp; development/blood ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Cytokines/metabolism/genetics/blood ; Bacteroidetes ; Metabolome ; Male ; East Asian People ; },
abstract = {Increasing evidence has indicated that the gut microbiome plays an important role in chicken growth traits. However, the cecal microbial taxa associated with the growth rates of the Chinese Ningdu yellow chickens are unknown. In this study, shotgun metagenomic sequencing was used to identify cecal bacterial species associated with the growth rate of the Chinese Ningdu yellow chickens. We found that nine cecal bacterial species differed significantly between high and low growth rate chickens, including three species (Succinatimonas hippei, Phocaeicola massiliensis, and Parabacteroides sp. ZJ-118) that were significantly enriched in high growth rate chickens. We identified six Bacteroidales that were significantly enriched in low growth rate chickens, including Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium which were key biomarkers in differentiating high and low growth rate chickens and were associated with alterations in the functional taxa of the cecal microbiome. Untargeted serum metabolome analysis revealed that 8 metabolites showing distinct enrichment patterns between high and low growth rate chickens, including triacetate lactone and N-acetyl-a-neuraminic acid, which were at higher concentrations in low growth rate chickens and were positively and significantly correlated with Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium. Furthermore, the results suggest that serum cytokines, such as IL-5, may reduce growth rate and are related to changes in serum metabolites and gut microbes (e.g., Barnesiella sp. An22 and Barnesiella sp. ET7). These results provide important insights into the effects of the cecal microbiome, serum metabolism and cytokines in Ningdu yellow chickens.},
}
@article {pmid38824761,
year = {2024},
author = {Alqawasmeh, OAM and Jiang, XT and Cong, L and Wu, W and Leung, MBW and Chung, JPW and Yim, HCH and Fok, EKL and Chan, DYL},
title = {Vertical transmission of microbiomes into embryo culture media and its association with assisted reproductive outcomes.},
journal = {Reproductive biomedicine online},
volume = {49},
number = {2},
pages = {103977},
doi = {10.1016/j.rbmo.2024.103977},
pmid = {38824761},
issn = {1472-6491},
mesh = {Humans ; Female ; Male ; *Microbiota ; Adult ; *Culture Media ; Pregnancy ; *Follicular Fluid/microbiology ; *Reproductive Techniques, Assisted ; *Semen/microbiology ; Embryo Culture Techniques ; Fertilization in Vitro ; Infertility, Female/microbiology/therapy ; },
abstract = {RESEARCH QUESTION: Can microbes vertically transmit from semen and follicular fluid to embryo culture media during assisted reproductive technology (ART) treatment?<br><br>DESIGN: Spent embryo culture media (SECM), seminal fluid and follicular fluid samples were collected from 61 couples with infertility undergoing ART treatment at the Prince of Wales Hospital, Hong Kong SAR, China. Metagenomic analysis was conducted using 16s rRNA sequencing to identify the source of microbes in SECM, correlation between the semen microbiome and male infertility, and correlation between the follicular fluid microbiome and female infertility.<br><br>RESULTS: Microbial vertical transmission into SECM was reported in 82.5% of cases, and semen was the main source of contamination in conventional IVF cases. The increased abundances of Staphylococcus spp. and Streptococcus anginosus in semen had negative impacts on total motility and sperm count, respectively (P < 0.001). Significant increases in abundance of the genera Prophyromonas, Neisseria and Facklamia were observed in follicular fluid in women with anovulation, uterine factor infertility and unexplained infertility, respectively (P < 0.01). No significant correlation was found between the bacteria identified in all sample types and ART outcomes, including fertilization rate, embryo development, number of available embryos, and clinical pregnancy rate.<br><br>CONCLUSION: Embryo culture media can be contaminated during ART treatment, not only by seminal microbes but also by follicular fluid and other sources of microbes. Strong correlations were found between specific microbial taxa in semen and sperm quality, and between the follicular fluid microbiome and the aetiology of female infertility. However, no significant association was found between the microbiomes of SECM, semen and follicular fluid and ART outcomes.},
}
@article {pmid37855614,
year = {2023},
author = {Lopes, AM and Abrantes, J},
title = {On the virome's hidden diversity: lessons from RHDV.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0197123},
pmid = {37855614},
issn = {2150-7511},
support = {PTDC/CVT-CVT/0143/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; CEECIND/01388/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; CEECIND/00078/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; },
mesh = {*Virome/genetics ; Humans ; *High-Throughput Nucleotide Sequencing ; Animals ; Metagenomics ; Reoviridae/genetics/classification/isolation &amp; purification ; Genetic Variation ; },
abstract = {Emerging infectious diseases are a major challenge to human and animal health. While predicting the emergence of pathogens is complex, the advent of high-throughput sequencing technologies has allowed the rapid identification of unknown microbiology diversity within organisms. Here, we discuss an example of a metatranscriptomics output to decipher viral evolution.},
}
@article {pmid37843286,
year = {2023},
author = {Claesen, J and Brown, JM},
title = {Predicting cardiovascular disease risk from gut microbial genes.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0197023},
pmid = {37843286},
issn = {2150-7511},
support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 DK130227/DK/NIDDK NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; R01 DK130227, R01 DK120679//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P50 AA024333/AA/NIAAA NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/genetics ; *Cardiovascular Diseases/genetics/microbiology/metabolism ; *Methylamines/metabolism ; Humans ; *Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics ; Risk Factors ; },
abstract = {Gut bacteria-driven production of trimethylamine (TMA) is strongly associated with cardiovascular disease. Borton et al. (mBio 14:e01511-23, 2023, https://doi.org/10.1128/mbio.01511-23) introduce the Methylated Amine Gene Inventory of Catabolism database (MAGICdb), comprehensively cataloging pathways involved in TMA metabolism. By integrating transcriptomics, proteomics, and metagenomic data, this work identifies key bacterial players in the process and can link gut microbial gene content to fecal TMA concentrations. This work shows that methylated amine metabolism is a keystone microbiome process carried out by a small proportion of the community. Proatherogenic pathways are more widely distributed among the gut microbiota, and new TMA-reducing genera were identified that might offer new potential for probiotic strategies or targeted microbiome interventions. Remarkably, MAGICdb's power to predict cardiovascular disease risk matches an approach using more traditional lipid risk factors. This open source will be a valuable tool for the community to link methylated amine metabolism to gut microbiome-related human health conditions.},
}
@article {pmid39065120,
year = {2024},
author = {Li, F and Lyu, H and Li, H and Xi, K and Yi, Y and Zhang, Y},
title = {Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp.},
journal = {Microorganisms},
volume = {12},
number = {7},
pages = {},
doi = {10.3390/microorganisms12071351},
pmid = {39065120},
issn = {2076-2607},
support = {Qiankehejichu-ZK[2022]Zhongdian 033//Natural Science Foundation of Guizhou Province/ ; 31960217,31902019, 32272022//National Natural Science Foundation of China/ ; },
abstract = {Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure.},
}
@article {pmid39054479,
year = {2024},
author = {Boldrini, L and Chiloiro, G and Di Franco, S and Romano, A and Smiljanic, L and Tran, EH and Bono, F and Charles Davies, D and Lopetuso, L and De Bonis, M and Minucci, A and Giacò, L and Cusumano, D and Placidi, L and Giannarelli, D and Sala, E and Gambacorta, MA},
title = {MOREOVER: multiomics MR-guided radiotherapy optimization in locally advanced rectal cancer.},
journal = {Radiation oncology (London, England)},
volume = {19},
number = {1},
pages = {94},
pmid = {39054479},
issn = {1748-717X},
support = {Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; },
mesh = {*Rectal Neoplasms/radiotherapy/pathology/therapy ; Humans ; Neoadjuvant Therapy/methods ; Gastrointestinal Microbiome ; Magnetic Resonance Imaging ; Radiotherapy, Image-Guided/methods ; Chemoradiotherapy/methods ; Circulating Tumor DNA/genetics ; Biomarkers, Tumor ; Genomics/methods ; Male ; Female ; Multiomics ; },
abstract = {BACKGROUND: Complete response prediction in locally advanced rectal cancer (LARC) patients is generally focused on the radiomics analysis of staging MRI. Until now, omics information extracted from gut microbiota and circulating tumor DNA (ctDNA) have not been integrated in composite biomarkers-based models, thereby omitting valuable information from the decision-making process. In this study, we aim to integrate radiomics with gut microbiota and ctDNA-based genomics tracking during neoadjuvant chemoradiotherapy (nCRT).<br><br>METHODS: The main hypothesis of the MOREOVER study is that the incorporation of composite biomarkers with radiomics-based models used in the THUNDER-2 trial will improve the pathological complete response (pCR) predictive power of such models, paving the way for more accurate and comprehensive personalized treatment approaches. This is due to the inclusion of actionable omics variables that may disclose previously unknown correlations with radiomics. Aims of this study are: - to generate longitudinal microbiome data linked to disease resistance to nCRT and postulate future therapeutic strategies in terms of both type of treatment and timing, such as fecal microbiota transplant in non-responding patients. - to describe the genomics pattern and ctDNA data evolution throughout the nCRT treatment in order to support the prediction outcome and identify new risk-category stratification agents. - to mine and combine collected data through integrated multi-omics approaches (radiomics, metagenomics, metabolomics, metatranscriptomics, human genomics, ctDNA) in order to increase the performance of the radiomics-based response predictive model for LARC patients undergoing nCRT on MR-Linac.<br><br>EXPERIMENTAL DESIGN: The objective of the MOREOVER project is to enrich the phase II THUNDER-2 trial (NCT04815694) with gut microbiota and ctDNA omics information, by exploring the possibility to enhance predictive performance of the developed model. Longitudinal ctDNA genomics, microbiome and genomics data will be analyzed on 7 timepoints: prior to nCRT, during nCRT on a weekly basis and prior to surgery. Specific modelling will be performed for data harvested, according to the TRIPOD statements.<br><br>DISCUSSION: We expect to find differences in fecal microbiome, ctDNA and radiomics profiles between the two groups of patients (pCR and not pCR). In addition, we expect to find a variability in the stability of the considered omics features over time. The identified profiles will be inserted into dedicated modelling solutions to set up a multiomics decision support system able to achieve personalized treatments.},
}
@article {pmid39052651,
year = {2024},
author = {Fofanova, TY and Karandikar, UC and Auchtung, JM and Wilson, RL and Valentin, AJ and Britton, RA and Grande-Allen, KJ and Estes, MK and Hoffman, K and Ramani, S and Stewart, CJ and Petrosino, JF},
title = {A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0300666},
doi = {10.1371/journal.pone.0300666},
pmid = {39052651},
issn = {1932-6203},
mesh = {Humans ; *Organoids/microbiology/metabolism ; *Oxygen/metabolism ; *Coculture Techniques/methods ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Gastrointestinal Microbiome ; Host Microbial Interactions ; Bacteria, Anaerobic/growth &amp; development/metabolism ; Intestines/microbiology/cytology ; Bacteroides thetaiotaomicron/metabolism ; },
abstract = {Mechanistic investigation of host-microbe interactions in the human gut are hindered by difficulty of co-culturing microbes with intestinal epithelial cells. On one hand the gut bacteria are a mix of facultative, aerotolerant or obligate anaerobes, while the intestinal epithelium requires oxygen for growth and function. Thus, a coculture system that can recreate these contrasting oxygen requirements is critical step towards our understanding microbial-host interactions in the human gut. Here, we demonstrate Intestinal Organoid Physoxic Coculture (IOPC) system, a simple and cost-effective method for coculturing anaerobic intestinal bacteria with human intestinal organoids (HIOs). Using commensal anaerobes with varying degrees of oxygen tolerance, such as nano-aerobe Bacteroides thetaiotaomicron and strict anaerobe Blautia sp., we demonstrate that IOPC can successfully support 24-48 hours HIO-microbe coculture. The IOPC recapitulates the contrasting oxygen conditions across the intestinal epithelium seen in vivo. The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease.},
}
@article {pmid39052319,
year = {2024},
author = {Liu, B and Qi, L and Zheng, Y and Zhang, C and Zhou, J and An, Z and Wang, B and Lin, Z and Yao, C and Wang, Y and Yin, G and Dong, H and Li, X and Liang, X and Han, P and Liu, M and Zhang, G and Cui, Y and Hou, L},
title = {Four years of climate warming reduced dark carbon fixation in coastal wetlands.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae138},
pmid = {39052319},
issn = {1751-7370},
abstract = {Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a four-year field warming experiment (average annual temperature increase of 1.5°C), DCF rates were observed to be significantly inhibited by warming in coastal wetlands (average annual DCF decline of 21.6%, and estimated annual loss of 0.08-1.5 Tg C yr-1 in global coastal marshes), thus causing a positive climate feedback. Under climate warming, chemoautotrophic microbial abundance and biodiversity, which were jointly affected by environmental changes such as soil organic carbon and water content, were recognized as significant drivers directly affecting DCF rates. Metagenomic analysis further revealed that climate warming may alter the pattern of DCF carbon sequestration pathways in coastal wetlands, increasing the relative importance of the 3HP/4HB cycle, whereas the relative importance of the dominant chemoautotrophic carbon fixation pathways (CBB cycle and W-L pathway) may decrease due to warming stress. Collectively, our work uncovers the feedback mechanism of microbially mediated DCF to climate warming in coastal wetlands, and emphasizes a decrease in carbon sequestration through DCF activities in this globally important ecosystem under a warming climate.},
}
@article {pmid39051424,
year = {2024},
author = {Ti, J and Ning, Z and Zhang, M and Wang, S and Gan, S and Xu, Z and Di, H and Kong, S and Sun, W and He, Z},
title = {Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {7},
pages = {e11085},
doi = {10.1002/wer.11085},
pmid = {39051424},
issn = {1554-7531},
support = {42330714//National Natural Science Foundation of China/ ; D2021504025//Natural Science Foundation of Hebei Province/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; *Petroleum ; Bacteria/classification/genetics/metabolism ; Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Biodiversity ; Water Microbiology ; },
abstract = {Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.},
}
@article {pmid39048979,
year = {2024},
author = {Jiang, C and Yang, J and Peng, X and Li, X},
title = {A permutable MLP-like architecture for disease prediction from gut metagenomic data.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {246},
pmid = {39048979},
issn = {1471-2105},
support = {82171526//National Natural Science Foundation of China/ ; 2020A38//Beijing Talents Fund/ ; SZU-BDSC-OF2024-19//National Engineering Laboratory for Big Data System Computing Technology/ ; },
mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Neural Networks, Computer ; Phylogeny ; Machine Learning ; Deep Learning ; Metagenome/genetics ; },
abstract = {Metagenomic data plays a crucial role in analyzing the relationship between microbes and diseases. However, the limited number of samples, high dimensionality, and sparsity of metagenomic data pose significant challenges for the application of deep learning in data classification and prediction. Previous studies have shown that utilizing the phylogenetic tree structure to transform metagenomic abundance data into a 2D matrix input for convolutional neural networks (CNNs) improves classification performance. Inspired by the success of a Permutable MLP-like architecture in visual recognition, we propose Metagenomic Permutator (MetaP), which applied the Permutable MLP-like network structure to capture the phylogenetic information of microbes within the 2D matrix formed by phylogenetic tree. Our experiments demonstrate that our model achieved competitive performance compared to other deep neural networks and traditional machine learning, and has good prospects for multi-classification and large sample sizes. Furthermore, we utilize the SHAP (SHapley Additive exPlanations) method to interpret our model predictions, identifying the microbial features that are associated with diseases.},
}
@article {pmid39047022,
year = {2024},
author = {Lekuya, HM and Kateete, DP and Olweny, G and Kigozi, E and Kamabu, LK and Mudekereza, SP and Nantambi, R and Mbiine, R and Makumbi, F and Cose, S and Vandersteene, J and Baert, E and Kalala, JO and Galukande, M},
title = {Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0303483},
doi = {10.1371/journal.pone.0303483},
pmid = {39047022},
issn = {1932-6203},
mesh = {Humans ; Male ; *Surgical Wound Infection/microbiology/epidemiology ; Female ; *Scalp/microbiology ; Adult ; *Microbiota/genetics ; *Metagenomics/methods ; *Brain Injuries, Traumatic/microbiology ; Prospective Studies ; Africa South of the Sahara/epidemiology ; Skin/microbiology ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Uganda/epidemiology ; Middle Aged ; Risk Factors ; Metagenome ; },
abstract = {BACKGROUND: Surgical site infections (SSI) are a significant concern following traumatic brain injury (TBI) surgery and often stem from the skin's microbiota near the surgical site, allowing bacteria to penetrate deeper layers and potentially causing severe infections in the cranial cavity. This study investigated the relationship between scalp skin microbiota composition and the risk of SSI after TBI surgery in sub-Saharan Africa (SSA).<br><br>METHODS: This was a prospective cohort study, enrolling patients scheduled for TBI surgery. Sterile skin swabs were taken from the surrounding normal skin of the head and stored for analysis at -80&#xb0;Celcius. Patients were monitored postoperatively for up to three months to detect any occurrences of SSI. 16S rRNA sequencing was used to analyze the skin microbiota composition, identifying different taxonomic microorganisms at the genus level. The analysis compared two groups: those who developed SSI and those who did not.<br><br>RESULTS: A total of 57 patients were included, mostly male (89.5%) with a mean age of 26.5 years, predominantly from urban areas in Uganda and victims of assault. Graphical visualization and metagenomic metrics analysis revealed differences in composition, richness, and evenness of skin microbiota within samples (&#x3b1;) or within the community (&#x3b2;), and showed specific taxa (phylum and genera) associated with either the group of SSI or the No SSI.<br><br>CONCLUSIONS: Metagenomic sequencing analysis uncovered several baseline findings and trends regarding the skin microbiome's relationship with SSI risk. There is an association between scalp microbiota composition (abundancy and diversity) and SSI occurrence following TBI surgery in SSA. We hypothesize under reserve that the scalp microbiota dysbiosis could potentially be an independent predictor of the occurrence of SSI; we advocate for further studies with larger cohorts.},
}
@article {pmid38977109,
year = {2024},
author = {Hu, L and Li, X and Li, C and Wang, L and Han, L and Ni, W and Zhou, P and Hu, S},
title = {Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut.},
journal = {Gene},
volume = {927},
number = {},
pages = {148758},
doi = {10.1016/j.gene.2024.148758},
pmid = {38977109},
issn = {1879-0038},
mesh = {Animals ; *Glycoside Hydrolases/genetics/metabolism/chemistry ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Horses ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Substrate Specificity ; Phylogeny ; },
abstract = {The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.},
}
@article {pmid38896886,
year = {2024},
author = {Yan, P and Zhuang, S and Li, M and Zhang, J and Wu, S and Xie, H and Wu, H},
title = {Combined environmental pressure induces unique assembly patterns of micro-plastisphere biofilm microbial communities in constructed wetlands.},
journal = {Water research},
volume = {260},
number = {},
pages = {121958},
doi = {10.1016/j.watres.2024.121958},
pmid = {38896886},
issn = {1879-2448},
mesh = {*Wetlands ; *Biofilms ; Microbiota ; Wastewater/microbiology ; Humic Substances ; Sulfamethoxazole ; Microplastics ; },
abstract = {The characteristics and dynamics of micro-plastisphere biofilm on the surface of microplastics (MPs) within artificial ecosystems, such as constructed wetlands (CWs), remain unclear, despite these ecosystems' potential to serve as sinks for MPs. This study investigates the dynamic evolution of micro-plastisphere biofilm in CWs, utilizing simulated wastewater containing sulfamethoxazole and humic acid, through physicochemical characterization and metagenomic analysis. Two different types of commercial plastics, including non-degradable polyethylene and degradable polylactic acid, were shredded into MPs and studied. The findings reveal that the types, shape and incubation time of MPs, along with humic acid content in wastewater, affected the quantity and quality of biofilms, such as the biofilm composition, spatial structure and microbial communities. After just 15 days into incubation, numerous microbials were observed on MP samples, with increases in biofilms content and enhanced humification of extracellular polymeric substances over time. Additionally, microbial communities on polylactic acid MPs, or those incubated for longer time, exhibit higher diversity, connectivity and stability, along with reduced vulnerability. Conversely, biofilms on polyethylene MPs were thicker, with higher potential for greenhouse gas emission and increased risk of antibiotic resistance genes. The addition of humic acid demonstrated opposite effects on biofilms across environmental interfaces, possibly due to its dual potential to produce light-induced free radicals and serve as a carbon source. Binning analysis further uncovered a unique assembly pattern of nutrients cycle genes and antibiotic resistance genes, significantly correlated within micro-plastisphere microbial communities, under the combined stress of nutrition and sulfamethoxazole. These results emphasize the shaping of micro-plastisphere biofilm characteristics by unique environmental conditions in artificial ecosystems, and the need to understand how DOM and other pollutants covary with MP pollution.},
}
@article {pmid38865893,
year = {2024},
author = {Wu, Z and Ji, Y and Liu, G and Yu, X and Shi, K and Liang, B and Freilich, S and Jiang, J},
title = {Electro-stimulation modulates syntrophic interactions in methanogenic toluene-degrading microbiota for enhanced functionality.},
journal = {Water research},
volume = {260},
number = {},
pages = {121898},
doi = {10.1016/j.watres.2024.121898},
pmid = {38865893},
issn = {1879-2448},
mesh = {*Microbiota ; *Methane/metabolism ; *Toluene/metabolism ; Biodegradation, Environmental ; },
abstract = {Syntrophy achieved via microbial cooperation is vital for anaerobic hydrocarbon degradation and methanogenesis. However, limited understanding of the metabolic division of labor and electronic interactions in electro-stimulated microbiota has impeded the development of enhanced biotechnologies for degrading hydrocarbons to methane. Here, compared to the non-electro-stimulated methanogenic toluene-degrading microbiota, electro-stimulation at 800 mV promoted toluene degradation and methane production efficiencies by 11.49 %-14.76 % and 75.58 %-290.11 %, respectively. Hydrocarbon-degrading gene bamA amplification and metagenomic sequencing analyses revealed that f_Syntrophobacteraceae MAG116 may act as a toluene degrader in the non-electro-stimulated microbiota, which was proposed to establish electron syntrophy with the acetoclastic methanogen Methanosarcina spp. (or Methanothrix sp.) through e-pili or shared acetate. In the electro-stimulated microbiota, 37.22 ± 4.33 % of Desulfoprunum sp. (affiliated f_Desulfurivibrionaceae MAG10) and 58.82 ± 3.74 % of the hydrogenotrophic methanogen Methanobacterium sp. MAG74 were specifically recruited to the anode and cathode, respectively. The potential electrogen f_Desulfurivibrionaceae MAG10 engaged in interspecies electron transfer with both syntroph f_Syntrophobacteraceae MAG116 and the anode, which might be facilitated by c-type cytochromes (e.g., ImcH, OmcT, and PilZ). Moreover, upon capturing electrons from the external circuit, the hydrogen-producing electrotroph Aminidesulfovibrio sp. MAG60 could share electrons and hydrogen with the methanogen Methanobacterium sp. MAG74, which uniquely harbored hydrogenase genes ehaA-R and ehbA-P. This study elucidates the microbial interaction mechanisms underlying the enhanced metabolic efficiency of the electro-stimulated methanogenic toluene-degrading microbiota, and emphasizes the significance of metabolic and electron syntrophic interactions in maintaining the stability of microbial community functionality.},
}
@article {pmid35268611,
year = {2022},
author = {Kabaivanova, L and Hubenov, V and Dimitrova, L and Simeonov, I and Wang, H and Petrova, P},
title = {Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {5},
pages = {},
pmid = {35268611},
issn = {1420-3049},
support = {Grant KP-06-IP-CHINA/3//Bulgarian National Science Fund/ ; 2021YFE0102700//Intergovernmental International Science and Technology Innovation Cooperation Key project of the National Key R&amp;D Program of China/ ; },
mesh = {Anaerobiosis ; *Archaea/metabolism/genetics ; *Methane/metabolism ; *Hydrogen/metabolism ; *Biofuels ; Bacteria/metabolism/genetics ; Bioreactors/microbiology ; Agriculture/methods ; Triticum/metabolism ; Biodegradation, Environmental ; Microbial Consortia/physiology ; },
abstract = {Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t[-1] compared to a 361.62 kWh·t[-1] cumulative yield of energy carrier for a one-stage process.},
}
@article {pmid34662347,
year = {2021},
author = {Herzog, EL and Wäfler, M and Keller, I and Wolf, S and Zinkernagel, MS and Zysset-Burri, DC},
title = {The importance of age in compositional and functional profiling of the human intestinal microbiome.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0258505},
pmid = {34662347},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Male ; Female ; Adult ; *Feces/microbiology ; Machine Learning ; Age Factors ; Metagenome ; Aged, 80 and over ; Aging ; Metagenomics/methods ; Young Adult ; },
abstract = {The intestinal microbiome plays a central role in human health and disease. While its composition is relatively stable throughout adulthood, the microbial balance starts to decrease in later life stages. Thus, in order to maintain a good quality of life, including the prevention of age-associated diseases in the elderly, it is important to understand the dynamics of the intestinal microbiome. In this study, stool samples of 278 participants were sequenced by whole metagenome shotgun sequencing and their taxonomic and functional profiles characterized. The two age groups, below65 and above65, could be separated based on taxonomic and associated functional features using Multivariate Association of Linear Models. In a second approach, through machine learning, biomarkers connecting the intestinal microbiome with age were identified. These results reflect the importance to select age-matched study groups for unbiased metagenomic data analysis and the possibility to generate robust data by applying independent algorithms for data analysis. Furthermore, since the intestinal microbiome can be modulated by antibiotics and probiotics, the data of this study may have implications on preventive strategies of age-associated degradation processes and diseases by microbiome-altering interventions.},
}
@article {pmid34524637,
year = {2022},
author = {Liu, J and Zuo, X and Peng, K and He, R and Yang, L and Liu, R},
title = {Biogas and Volatile Fatty Acid Production During Anaerobic Digestion of Straw, Cellulose, and Hemicellulose with Analysis of Microbial Communities and Functions.},
journal = {Applied biochemistry and biotechnology},
volume = {194},
number = {2},
pages = {762-782},
pmid = {34524637},
issn = {1559-0291},
support = {21808010//National Natural Science Foundation of China/ ; 2018YFE111000//Key Technologies Research and Development Program/ ; },
mesh = {*Cellulose/metabolism ; *Fatty Acids, Volatile/metabolism ; *Polysaccharides/metabolism ; *Biofuels ; Anaerobiosis ; Methane/metabolism/biosynthesis ; Microbiota ; Oryza/metabolism ; },
abstract = {The anaerobic digestion efficiency and methane production of straw was limited by its complex composition and structure. In this study, rice straw (RS), cellulose, and hemicellulose were used as raw materials to study biogas production performance and changes in the volatile fatty acids (VFAs). Further, microbial communities and genetic functions were analyzed separately for each material. The biogas production potential of RS, cellulose, and hemicellulose was different, with cumulative biogas production of 283.75, 412.50, and 620.64 mL/(g·VS), respectively. The methane content of the biogas produced from cellulose and hemicellulose was approximately 10% higher than that produced from RS after the methane content stabilized. The accumulation of VFAs occurred in the early stage of anaerobic digestion in all materials, and the cumulative amount of VFAs in both cellulose and hemicellulose was relatively higher than that in RS, and the accumulation time was 12 and 14 days longer, respectively. When anaerobic digestion progressed to a stable stage, Clostridium was the dominant bacterial genus in all three anaerobic digestion systems, and the abundance of Ruminofilibacter was higher during anaerobic digestion of RS. Genetically, anaerobic digestion of all raw materials proceeded mainly via aceticlastic methanogenesis, with similar functional components. The different performance of anaerobic digestion of RS, cellulose, and hemicellulose mainly comes from the difference of composition of raw materials. Increasing the accessibility of cellulose and hemicellulose in RS feedstock by pretreatment is an effective way to improve the efficiency of anaerobic digestion. Since the similar microbial community structure will be acclimated during anaerobic digestion, there is no need to adjust the initial inoculum when the accessibility of cellulose and hemicellulose changes.},
}
@article {pmid34474998,
year = {2021},
author = {Liu, C and Hu, J and Wu, Y and Irwin, DM and Chen, W and Zhang, Z and Yu, L},
title = {Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {48},
number = {9},
pages = {825-835},
doi = {10.1016/j.jgg.2021.07.009},
pmid = {34474998},
issn = {1673-8527},
mesh = {*Pangolins/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animals, Wild ; Breeding ; Endangered Species ; Anti-Bacterial Agents/administration &amp; dosage ; Diet ; RNA, Ribosomal, 16S/analysis/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Virulence Factors/analysis ; Carbohydrate Metabolism ; Enzymes/analysis ; },
abstract = {Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.},
}
@article {pmid34391676,
year = {2021},
author = {Chen, C and Hao, L and Zhang, Z and Tian, L and Zhang, X and Zhu, J and Jie, Z and Tong, X and Xiao, L and Zhang, T and Jin, X and Xu, X and Yang, H and Wang, J and Kristiansen, K and Jia, H},
title = {Cervicovaginal microbiome dynamics after taking oral probiotics.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {48},
number = {8},
pages = {716-726},
doi = {10.1016/j.jgg.2021.03.019},
pmid = {34391676},
issn = {1673-8527},
mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; *Vagina/microbiology ; *Microbiota/genetics/drug effects ; Adult ; Dysbiosis/microbiology/therapy ; Administration, Oral ; Cervix Uteri/microbiology ; Middle Aged ; },
abstract = {The vaginal microbiota is less complex than the gut microbiota, and the colonization of Lactobacillus in the female vagina is considered to be critical for reproductive health. Oral probiotics have been suggested as promising means to modulate vaginal homeostasis in the general population. In this study, 60 Chinese women were followed for over a year before, during, and after treatment with the probiotics Lactobacillus rhamnosus GR-1 and Lactobacillusreuteri RC-14. Shotgun metagenomic data of 1334 samples from multiple body sites did not support a colonization route of the probiotics from the oral cavity to the intestinal tract and then to the vagina. Our analyses enable the classification of the cervicovaginal microbiome into a stable state and a state of dysbiosis. The microbiome in the stable group steadily maintained a relatively high abundance of Lactobacilli over one year, which was not affected by probiotic intake, whereas in the dysbiosis group, the microbiota was more diverse and changed markedly over time. Data from a subset of the dysbiosis group suggests this subgroup possibly benefited from supplementation with the probiotics, indicating that probiotics supplementation can be prescribed for women in a subclinical microbiome setting of dysbiosis, providing opportunities for targeted and personalized microbiome reconstitution.},
}
@article {pmid34381207,
year = {2021},
author = {Fremin, BJ and Nicolaou, C and Bhatt, AS},
title = {Simultaneous ribosome profiling of hundreds of microbes from the human microbiome.},
journal = {Nature protocols},
volume = {16},
number = {10},
pages = {4676-4691},
pmid = {34381207},
issn = {1750-2799},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; P30 AG047366//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 AG066515/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Ribosomes/metabolism/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; Ribosome Profiling ; },
abstract = {Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality (https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.},
}
@article {pmid34341379,
year = {2021},
author = {Bel Lassen, P and Belda, E and Prifti, E and Dao, MC and Specque, F and Henegar, C and Rinaldi, L and Wang, X and Kennedy, SP and Zucker, JD and Calame, W and Lamarche, B and Claus, SP and Clément, K},
title = {Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15620},
pmid = {34341379},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Intra-Abdominal Fat/metabolism ; *Dietary Supplements ; Adult ; Middle Aged ; *Amino Acids/metabolism ; *Caloric Restriction/methods ; Double-Blind Method ; Dietary Proteins/administration &amp; dosage/metabolism ; Energy Metabolism ; },
abstract = {Interactions between diet and gut microbiota are critical regulators of energy metabolism. The effects of fibre intake have been deeply studied but little is known about the impact of proteins. Here, we investigated the effects of high protein supplementation (Investigational Product, IP) in a double blind, randomised placebo-controled intervention study (NCT01755104) where 107 participants received the IP or an isocaloric normoproteic comparator (CP) alongside a mild caloric restriction. Gut microbiota profiles were explored in a patient subset (n = 53) using shotgun metagenomic sequencing. Visceral fat decreased in both groups (IP group: - 20.8 ± 23.2 cm[2]; CP group: - 14.5 ± 24.3 cm[2]) with a greater reduction (p < 0.05) with the IP supplementation in the Per Protocol population. Microbial diversity increased in individuals with a baseline low gene count (p < 0.05). The decrease in weight, fat mass and visceral fat mass significantly correlated with the increase in microbial diversity (p < 0.05). Protein supplementation had little effects on bacteria composition but major differences were seen at functional level. Protein supplementation stimulated bacterial amino acid metabolism (90% amino-acid synthesis functions enriched with IP versus 13% in CP group (p < 0.01)). Protein supplementation alongside a mild energy restriction induces visceral fat mass loss and an activation of gut microbiota amino-acid metabolism.Clinical trial registration: NCT01755104 (24/12/2012). https://clinicaltrials.gov/ct2/show/record/NCT01755104?term=NCT01755104&amp;draw=2&amp;rank=1 .},
}
@article {pmid34283837,
year = {2021},
author = {Velasco, C and Dunn, C and Sturdy, C and Izda, V and Martin, J and Rivas, A and McNaughton, J and Jeffries, MA},
title = {Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0248322},
pmid = {34283837},
issn = {1932-6203},
support = {K08 AR070891/AR/NIAMS NIH HHS/United States ; P20 GM125528/GM/NIGMS NIH HHS/United States ; R01 AR076440/AR/NIAMS NIH HHS/United States ; R61 AR078075/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Wound Healing ; Mice ; Female ; Male ; *Mice, Inbred C57BL ; Ear/microbiology ; Fecal Microbiota Transplantation ; Cecum/microbiology ; },
abstract = {OBJECTIVE: Adult elastic cartilage has limited repair capacity. MRL/MpJ (MRL) mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and non-healer mice and to evaluate whether this healing phenotype can be transferred via gut microbiome transplantation.<br><br>METHODS: We orally transplanted C57BL/6J (B6) mice with MRL/MpJ cecal contents at weaning and as adults (n = 57) and measured ear hole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n = 25) and B6-transplanted MRL (n = 20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n = 58), cecal microbiomes were profiled by 16S sequencing and compared to ear hole closure. Microbial metagenomes were imputed using PICRUSt.<br><br>RESULTS: Transplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved ear hole closure. B6-vehicle mice healed ear hole punches poorly (0.25&#xb1;0.03mm, mm ear hole healing 4 weeks after a 2mm ear hole punch [2.0mm-final ear hole size], mean&#xb1;SEM), whereas MRL-vehicle mice healed well (1.4&#xb1;0.1mm). MRL-transplanted B6 mice healed roughly three times as well as B6-vehicle mice, and half as well as MRL-vehicle mice (0.74&#xb1;0.05mm, P = 6.9E-10 vs. B6-vehicle, P = 5.2E-12 vs. MRL-vehicle). Transplantation of MRL mice with B6 cecal material did not reduce MRL healing (B6-transplanted MRL 1.3&#xb1;0.1 vs. MRL-vehicle 1.4&#xb1;0.1, p = 0.36). Transplantation prior to ear punch was associated with the greatest ear hole closure. Offspring of transplanted mice healed significantly better than non-transplanted control mice (offspring:0.63&#xb1;0.03mm, mean&#xb1;SEM vs. B6-vehicle control:0.25&#xb1;0.03mm, n = 39 offspring, P = 4.6E-11). Several microbiome clades were correlated with healing, including Firmicutes (R = 0.84, P = 8.0E-7), Lactobacillales (R = 0.65, P = 1.1E-3), and Verrucomicrobia (R = -0.80, P = 9.2E-6). Females of all groups tended to heal better than males (B6-vehicle P = 0.059, MRL-transplanted B6 P = 0.096, offspring of MRL-transplanted B6 P = 0.0038, B6-transplanted MRL P = 1.6E-6, MRL-vehicle P = 0.0031). Many clades characteristic of female mouse cecal microbiota vs. males were the same as clades characteristic of MRL and MRL-transplanted B6 mice vs. B6 controls, including including increases in Clostridia and reductions in Verrucomicrobia in female mice.<br><br>CONCLUSION: In this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to non-healer mice via microbiome transplantation. We identified several microbiome clades associated with healing.},
}
@article {pmid34283836,
year = {2021},
author = {Huang, CY and Yu, WS and Liu, GC and Hung, SC and Chang, JH and Chang, JC and Cheng, CL and Sun, DS and Lin, MD and Lin, WY and Tzeng, YJ and Chang, HH},
title = {Opportunistic gill infection is associated with TiO2 nanoparticle-induced mortality in zebrafish.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0247859},
pmid = {34283836},
issn = {1932-6203},
mesh = {Animals ; *Zebrafish/microbiology ; *Titanium/toxicity ; *Gills/microbiology/drug effects ; Nanoparticles/toxicity ; Opportunistic Infections/microbiology ; Fish Diseases/microbiology/chemically induced/mortality ; Bacterial Load ; Metal Nanoparticles/toxicity ; Gastrointestinal Microbiome/drug effects ; },
abstract = {The large amounts of engineered titanium dioxide nanoparticles (TiO2NPs) that have been manufactured have inevitably been released into the ecosystem. Reports have suggested that TiO2 is a relatively inert material that has low toxicity to animals. However, as various types of NPs increasingly accumulate in the ocean, their effects on aquatic life-forms remain unclear. In this study, a zebrafish model was used to investigate TiO2NP-induced injury and mortality. We found that the treatment dosages of TiO2NP are positively associated with increased motility of zebrafish and the bacterial counts in the water. Notably, gill but not dorsal fin and caudal fin of the zebrafish displayed considerably increased bacterial load. Metagenomic analysis further revealed that gut microflora, such as phyla Proteobacteria, Bacteroidetes, and Actinobacteria, involving more than 95% of total bacteria counts in the NP-injured zebrafish gill samples. These results collectively suggest that opportunistic bacterial infections are associated with TiO2NP-induced mortality in zebrafish. Infections secondary to TiO2NP-induced injury could be a neglected factor determining the detrimental effects of TiO2NPs on wild fish.},
}
@article {pmid34252073,
year = {2021},
author = {Verma, S and Dutta, SK and Firnberg, E and Phillips, L and Vinayek, R and Nair, PP},
title = {Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0251590},
pmid = {34252073},
issn = {1932-6203},
mesh = {Humans ; *Fecal Microbiota Transplantation ; Female ; Male ; *Clostridium Infections/therapy/microbiology ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Feces/microbiology ; Gastrointestinal Microbiome ; Clostridioides difficile/genetics/isolation &amp; purification ; Recurrence ; Bacteria/genetics/classification/isolation &amp; purification ; Dysbiosis/microbiology/therapy ; Metagenome ; },
abstract = {BACKGROUND: Recurrent Clostridioides diffícile infection (RCDI) is associated with major bacterial dysbiosis and colitis. Fecal microbiota transplantation (FMT) is a highly effective therapeutic modality for RCDI. While several studies have identified bacterial species associated with resolution of symptoms in patients, characterization of the fecal microbiome at the bacterial strain level in RCDI patients before and after FMT and healthy donors, has been lacking. The aim of this study was to examine the ability of bacterial strains from healthy donors to engraft in the gastrointestinal tract of patients with RCDI following FMT.<br><br>METHODS: Fecal samples were collected from 22 patients with RCDI before and after FMT and their corresponding healthy donors. Total DNA was extracted from each sample and analyzed by shotgun metagenomic sequencing. The Cosmos-ID analysis platform was used for taxonomic assignment of sequences and calculation of the relative abundance (RA) of bacterial species and strains. From these data, the total number of bacterial strains (BSI), Shannon diversity index, dysbiosis index (DI), and bacterial engraftment factor, were calculated for each strain.<br><br>FINDINGS: A marked reduction (p<0&#xb7;0001) in the RA of total and specific bacterial strains, especially from phylum Firmicutes, was observed in RCDI patients prior to FMT. This change was associated with an increase in the DI (p<0&#xb7;0001) and in pathobiont bacterial strains from phylum Proteobacteria, such as Escherichia coli O157:H7 and Klebsiella pneumoniae UCI 34. BSI was significantly lower in this group of patients as compared to healthy donors and correlated with the Shannon Index. (p<0&#xb7;0001). Identification and engraftment of bacterial strains from healthy donors revealed a greater diversity and higher relative abundance of short-chain fatty acid (SCFA)-producing bacterial strains, including Lachnospiraceae bacterium 5_1_63FAA_u_t, Dorea formicigenerans ATCC 27755, Anaerostipes hadrusand others, in RCDI patients after FMT.<br><br>INTERPRETATION: These observations identify a group of SCFA-producing bacterial strains from healthy donors that engraft well in patients with RCDI following FMT and are associated with complete resolution of clinical symptoms and bacterial dysbiosis.},
}
@article {pmid34061881,
year = {2021},
author = {Ibekwe, AM and Ors, S and Ferreira, JFS and Liu, X and Suarez, DL},
title = {Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0252242},
pmid = {34061881},
issn = {1932-6203},
mesh = {*Seasons ; *Spinacia oleracea/microbiology ; *Salinity ; *Plant Leaves/microbiology ; *Bacteria/genetics/metabolism/classification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; },
abstract = {The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.},
}
@article {pmid33831065,
year = {2021},
author = {Crowe, SA and Simister, RL and Spence, JS and Kenward, PA and Van Slyke, AC and Lennox, P and Carr, N},
title = {Microbial community compositions in breast implant biofilms associated with contracted capsules.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0249261},
pmid = {33831065},
issn = {1932-6203},
mesh = {*Biofilms/growth &amp; development ; *Breast Implants/microbiology/adverse effects ; Humans ; Female ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics/classification/isolation &amp; purification ; Implant Capsular Contracture/microbiology ; Adult ; },
abstract = {Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation failure due to capsular contracture, and while these infections are generally ascribed to common skin commensals, this remains largely unsubstantiated through robust cultivation independent analyses. To determine capsule biofilm microbial community compositions, we employed amplicon sequencing of the 16S rRNA gene using DNA extracted from breast implant capsule samples. These cultivation independent analyses revealed that capsule associated biofilms are more diverse than canonical single-species infections, but have relatively low diversity (~ <100 species) compared to many host-associated microbial communities. In addition to taxa commonly associated with capsular contracture, the biofilms analyzed comprised a number of taxa that escaped detection in cultivation-dependent work. We have also isolated several key taxa identified through the culture-independent analyses. Together our analyses reveal that capsule biofilms are more diverse than cultivation studies suggest and can be heterogeneous within an individual capsule, between breasts of the same patient, across similar implant types, and over a range in severity of contracture. The complex nature of these communities requires further study across a broader suite of patients in addition to higher resolution analyses including metagenomics to better assess the fundamental role of microorganisms in capsular contracture.},
}
@article {pmid33587919,
year = {2021},
author = {Honarbakhsh, M and Ericsson, A and Zhong, G and Isoherranen, N and Zhu, C and Bromberg, Y and Van Buiten, C and Malta, K and Joseph, L and Sampath, H and Lackey, AI and Storch, J and Vetriani, C and Chikindas, ML and Breslin, P and Quadro, L},
title = {Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions.},
journal = {Journal of lipid research},
volume = {62},
number = {},
pages = {100046},
pmid = {33587919},
issn = {1539-7262},
support = {R01 GM111772/GM/NIGMS NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; R01 DK038389/DK/NIDDK NIH HHS/United States ; R01 HD083331/HD/NICHD NIH HHS/United States ; U54 AR055073/AR/NIAMS NIH HHS/United States ; R01 HD094778/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; *Vitamin A/metabolism ; Mice ; *Homeostasis ; Vitamin A Deficiency/metabolism ; Retinoids/metabolism ; Biological Transport ; Acyltransferases/metabolism/deficiency/genetics ; Intestinal Mucosa/metabolism ; Mice, Knockout ; Gastrointestinal Microbiome ; Retinol-Binding Proteins/metabolism ; Intestines ; },
abstract = {Lecithin:retinol acyltransferase and retinol-binding protein enable vitamin A (VA) storage and transport, respectively, maintaining tissue homeostasis of retinoids (VA derivatives). The precarious VA status of the lecithin:retinol acyltransferase-deficient (Lrat[-/-]) retinol-binding protein-deficient (Rbp[-/-]) mice rapidly deteriorates upon dietary VA restriction, leading to signs of severe vitamin A deficiency (VAD). As retinoids impact gut morphology and functions, VAD is often linked to intestinal pathological conditions and microbial dysbiosis. Thus, we investigated the contribution of VA storage and transport to intestinal retinoid homeostasis and functionalities. We showed the occurrence of intestinal VAD in Lrat[-/-]Rbp[-/-] mice, demonstrating the critical role of both pathways in preserving gut retinoid homeostasis. Moreover, in the mutant colon, VAD resulted in a compromised intestinal barrier as manifested by reduced mucins and antimicrobial defense, leaky gut, increased inflammation and oxidative stress, and altered mucosal immunocytokine profiles. These perturbations were accompanied by fecal dysbiosis, revealing that the VA status (sufficient vs. deficient), rather than the amount of dietary VA per se, is likely a major initial discriminant of the intestinal microbiome. Our data also pointed to a specific fecal taxonomic profile and distinct microbial functionalities associated with VAD. Overall, our findings revealed the suitability of the Lrat[-/-]Rbp[-/-] mice as a model to study intestinal dysfunctions and dysbiosis promoted by changes in tissue retinoid homeostasis induced by the host VA status and/or intake.},
}
@article {pmid39045787,
year = {2024},
author = {Tayebwa, DS and Hyeroba, D and Dunn, CD and Dunay, E and Richard, JC and Biryomumaisho, S and Acai, JO and Goldberg, TL},
title = {Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife.},
journal = {The Journal of general virology},
volume = {105},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002011},
pmid = {39045787},
issn = {1465-2099},
mesh = {Animals ; Dogs ; Uganda/epidemiology ; *Dog Diseases/virology/epidemiology/transmission ; Prevalence ; *Animals, Wild/virology ; Virome ; Viruses/classification/isolation &amp; purification/genetics ; Metagenomics ; Anelloviridae/genetics/isolation &amp; purification/classification ; Humans ; Virus Diseases/epidemiology/veterinary/transmission/virology ; },
abstract = {Domestic dogs (Canis lupus familiaris) live with humans, frequently contact other animals and may serve as intermediary hosts for the transmission of viruses. Free-roaming dogs, which account for over 70% of the world's domestic dog population, may pose a particularly high risk in this regard. We conducted an epidemiological study of dog viromes in three locations in Uganda, representing low, medium and high rates of contact with wildlife, ranging from dogs owned specifically for traditional hunting in a biodiversity and disease 'hotspot' to pets in an affluent suburb. We quantified rates of contact between dogs and wildlife through owner interviews and conducted canine veterinary health assessments. We then applied broad-spectrum viral metagenomics to blood plasma samples, from which we identified 46 viruses, 44 of which were previously undescribed, in three viral families, Sedoreoviridae, Parvoviridae and Anelloviridae. All 46 viruses (100 %) occurred in the high-contact population of dogs compared to 63 % and 39 % in the medium- and low-contact populations, respectively. Viral prevalence ranged from 2.1 % to 92.0 % among viruses and was highest, on average, in the high-contact population (22.3 %), followed by the medium-contact (12.3 %) and low-contact (4.8 %) populations. Viral richness (number of viruses per dog) ranged from 0 to 27 and was markedly higher, on average, in the high-contact population (10.2) than in the medium-contact (5.7) or low-contact (2.3) populations. Viral richness was strongly positively correlated with the number of times per year that a dog was fed wildlife and negatively correlated with the body condition score, body temperature and packed cell volume. Viral abundance (cumulative normalized metagenomic read density) varied 124-fold among dogs and was, on average, 4.1-fold higher and 2.4-fold higher in the high-contact population of dogs than in the low-contact or medium-contact populations, respectively. Viral abundance was also strongly positively correlated with the number of times per year that a dog was fed wildlife, negatively correlated with packed cell volume and positively correlated with white blood cell count. These trends were driven by nine viruses in the family Anelloviridae, genus Thetatorquevirus, and by one novel virus in the family Sedoreoviridae, genus Orbivirus. The genus Orbivirus contains zoonotic viruses and viruses that dogs can acquire through ingestion of infected meat. Overall, our findings show that viral prevalence, richness and abundance increased across a gradient of contact between dogs and wildlife and that the health status of the dog modified viral infection. Other ecological, geographic and social factors may also have contributed to these trends. Our finding of a novel orbivirus in dogs with high wildlife contact supports the idea that free-roaming dogs may serve as intermediary hosts for viruses of medical importance to humans and other animals.},
}
@article {pmid39044909,
year = {2024},
author = {Moumen, B and Samba-Louaka, C and Kimpamboudi, VAM and Boumba, AM and Ngoma, HS and Samba-Louaka, A},
title = {Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo.},
journal = {Data in brief},
volume = {55},
number = {},
pages = {110655},
pmid = {39044909},
issn = {2352-3409},
abstract = {After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.},
}
@article {pmid39044261,
year = {2024},
author = {Ma, S and Yin, Y and Guo, Y and Yao, C and Xu, S and Luo, Q and Yin, G and Wang, S and Wang, Q and Chen, H and Wang, R and Jin, L and Liang, G and Wang, H},
title = {The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {137},
pmid = {39044261},
issn = {2049-2618},
mesh = {Humans ; Male ; Female ; *DNA Viruses/isolation &amp; purification/genetics ; Middle Aged ; *Virus Diseases/blood/virology ; Adult ; *Hematologic Diseases/complications/blood ; *RNA Viruses/isolation &amp; purification ; Virome ; Aged ; Torque teno virus/isolation &amp; purification/genetics ; Cohort Studies ; Herpesvirus 4, Human/genetics/isolation &amp; purification ; Young Adult ; },
abstract = {BACKGROUND: Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features.<br><br>RESULTS: A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections.<br><br>CONCLUSIONS: Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.},
}
@article {pmid39044244,
year = {2024},
author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O},
title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {138},
pmid = {39044244},
issn = {2049-2618},
mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.<br><br>RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.<br><br>CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.},
}
@article {pmid39040604,
year = {2024},
author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S},
title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1390088},
pmid = {39040604},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation &amp; purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; },
abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.<br><br>METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.<br><br>RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.},
}
@article {pmid39039586,
year = {2024},
author = {Liang, JL and Feng, SW and Jia, P and Lu, JL and Yi, X and Gao, SM and Wu, ZH and Liao, B and Shu, WS and Li, JT},
title = {Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {136},
pmid = {39039586},
issn = {2049-2618},
support = {42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2023YFC3207300//National Key R&amp;D Program of China/ ; },
mesh = {China ; *Soil Microbiology ; *Metagenome ; *Ecosystem ; *Giant Viruses/genetics/classification ; Soil/chemistry ; Phylogeny ; Genome, Viral/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.<br><br>RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.<br><br>CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.},
}
@article {pmid39039555,
year = {2024},
author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T},
title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {134},
pmid = {39039555},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; },
abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.<br><br>RESULTS: We uncovered distinct distribution&#xa0;patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as&#xa0;potentially host abundance- or phage/host ratio-driven phage population changes.<br><br>CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.},
}
@article {pmid39039462,
year = {2024},
author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y},
title = {Gut microbiota and metabolic changes in children with idiopathic short stature.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {468},
pmid = {39039462},
issn = {1471-2431},
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.<br><br>METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.<br><br>RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC&#x2009;=&#x2009;0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.<br><br>CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.},
}
@article {pmid39039075,
year = {2024},
author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J},
title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6012},
pmid = {39039075},
issn = {2041-1723},
support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l&apos;innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; },
abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.},
}
@article {pmid39038938,
year = {2024},
author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC},
title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
pmid = {39038938},
issn = {1477-4054},
support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; },
mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; },
abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.},
}
@article {pmid39038883,
year = {2024},
author = {Han, PJ and Song, L and Wen, Z and Zhu, HY and Wei, YH and Wang, JW and Bai, M and Luo, LJ and Wang, JW and Chen, SX and You, XL and Han, DY and Bai, FY},
title = {Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences.},
journal = {Food microbiology},
volume = {123},
number = {},
pages = {104566},
doi = {10.1016/j.fm.2024.104566},
pmid = {39038883},
issn = {1095-9998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Fermentation ; China ; Microbiota ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; Metagenome ; Fermented Foods/microbiology ; },
abstract = {Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.},
}
@article {pmid39038849,
year = {2024},
author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Global compositional and functional states of the human gut microbiome in health and disease.},
journal = {Genome research},
volume = {34},
number = {6},
pages = {967-978},
doi = {10.1101/gr.278637.123},
pmid = {39038849},
issn = {1549-5469},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Metagenomics/methods ; Machine Learning ; Fusobacterium nucleatum/genetics ; Bacteria/classification/genetics ; },
abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.},
}
@article {pmid39037634,
year = {2024},
author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH},
title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {9},
pages = {276},
pmid = {39037634},
issn = {1573-0972},
support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; },
abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.},
}
@article {pmid39035870,
year = {2024},
author = {Rabbachin, L and Nir, I and Waldherr, M and Vassallo, Y and Piñar, G and Graf, A and Kushmaro, A and Sterflinger, K},
title = {Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.},
journal = {Frontiers in fungal biology},
volume = {5},
number = {},
pages = {1400380},
pmid = {39035870},
issn = {2673-6128},
abstract = {The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.},
}
@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}
@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.<br><br>RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).<br><br>CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}
@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}
@article {pmid39030599,
year = {2024},
author = {Xu, SY and Feng, XR and Zhao, W and Bi, YL and Diao, QY and Tu, Y},
title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {131},
pmid = {39030599},
issn = {2049-2618},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Weaning ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Female ; Fermentation ; Metagenomics/methods ; Metabolomics ; Fatty Acids, Volatile/metabolism/analysis ; Weight Gain ; Butyrates/metabolism ; },
abstract = {BACKGROUND: The average daily gain (ADG) of preweaning calves significantly influences their adult productivity and reproductive performance. Gastrointestinal microbes are known to exert an impact on host phenotypes, including ADG. The aim of this study was to investigate the mechanisms by which gastrointestinal microbiome regulate ADG in preweaning calves and to further validate them by isolating ADG-associated rumen microbes in vitro.<br><br>RESULTS: Sixteen Holstein heifer calves were selected from a cohort with 106 calves and divided into higher ADG (HADG; n&#x2009;=&#x2009;8) and lower ADG (LADG; n&#x2009;=&#x2009;8) groups. On the day of weaning, samples of rumen contents, hindgut contents, and plasma were collected for rumen metagenomics, rumen metabolomics, hindgut metagenomics, hindgut metabolomics, and plasma metabolomics analyses. Subsequently, rumen contents of preweaning Holstein heifer calves from the same dairy farm were collected to isolate ADG-associated rumen microbes. The results showed that the rumen microbes, including Pyramidobacter sp. C12-8, Pyramidobacter sp. CG50-2, Pyramidobacter porci, unclassified_g_Pyramidobacter, Pyramidobacter piscolens, and Acidaminococcus fermentans, were enriched in the rumen of HADG calves (LDA&#x2009;>&#x2009;2, P&#x2009;<&#x2009;0.05). Enrichment of these microbes in HADG calves' rumen promoted carbohydrate degradation and volatile fatty acid production, increasing proportion of butyrate in the rumen and ultimately contributing to higher preweaning ADG in calves (P&#x2009;<&#x2009;0.05). The presence of active carbohydrate degradation in the rumen was further suggested by the negative correlation of the rumen microbes P. piscolens, P. sp. C12-8 and unclassified_g_Pyramidobacter with the rumen metabolites D-fructose (R&#x2009;<&#x2009;&#x2009;-&#x2009;0.50, P&#x2009;<&#x2009;0.05). Widespread positive correlations were observed between rumen microbes (such as P. piscolens, P. porci, and A. fermentans) and beneficial plasma metabolites (such as 1-pyrroline-5-carboxylic acid and 4-fluoro-L-phenylalanine), which were subsequently positively associated with the growth rate of HADG calves (R&#x2009;>&#x2009;0.50, P&#x2009;<&#x2009;0.05). We succeeded in isolating a strain of A. fermentans from the rumen contents of preweaning calves and named it Acidaminococcus fermentans P41. The in vitro cultivation revealed its capability to produce butyrate. In vitro fermentation experiments demonstrated that the addition of A. fermentans P41 significantly increased the proportion of butyrate in the rumen fluid (P&#x2009;<&#x2009;0.05). These results further validated our findings. The relative abundance of Bifidobacterium pseudolongum in the hindgut of HADG calves was negatively correlated with hindgut 4-hydroxyglucobrassicin levels, which were positively correlated with plasma 4-hydroxyglucobrassicin levels, and plasma 4-hydroxyglucobrassicin levels were positively correlated with ADG (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: This study's findings unveil that rumen and hindgut microbes play distinctive roles in regulating the preweaning ADG of Holstein heifer calves. Additionally, the successful isolation of A. fermentans P41 not only validated our findings but also provided a valuable strain resource for modulating rumen microbes in preweaning calves. Video Abstract.},
}
@article {pmid39028528,
year = {2024},
author = {Han, Y and Zhang, Y and Yang, Z and Zhang, Q and He, X and Song, Y and Tian, L and Wu, H},
title = {Improving Aerobic Digestion of Food Waste by Adding a Personalized Microbial Inoculum.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {277},
pmid = {39028528},
issn = {1432-0991},
support = {236Z3301G//Natural Science Foundation of Hebei Province/ ; B2020203005//Natural Science Foundation of Hebei Province/ ; 2021LGQN027//Cultivation Project for Basic Research and Innovation of YanShan University/ ; 236Z3604G//National Science Founbdation of Hebei Province/ ; 2023GJJG396//Hebei Education Department/ ; ZD2022088//China Hebei Education Department/ ; ZC2023041//China Hebei Education Department/ ; 2021LGQN018//Cultivation Project for Basic Research and Innovation of YanShan University/ ; },
mesh = {Aerobiosis ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Microbial Consortia ; Garbage ; China ; Refuse Disposal/methods ; Hydrolysis ; Metagenomics ; Food Loss and Waste ; },
abstract = {In the context of China's garbage classification policy, on-site aerobic food waste (FW) digestion is crucial for reducing transportation and disposal costs. The efficiency of this process is largely determined by the microbial community structure and its functions. Therefore, this study aimed to analyze the impact of a personalized microbial consortium (MCM) on the efficiency of aerobic FW digestion and to reveal the underlying mechanisms. An MCM, sourced from naturally degrading FW, was selected to enrich degrading bacteria with relatively high hydrolyzing ability. The functionality of the MCM was evaluated by tracing the successions of microbial communities, and comparing the differences in the forms of organic compounds, metabolic functions, and hydrolase activities. X-ray photoelectron spectroscopy demonstrated that the MCM metabolized faster, and produced more acidic metabolites. Metagenomic analysis indicated that FW inoculated with the personalized MCM increased abundance of Bacillaceae producing hydrolysis enzymes and promoted glycolysis metabolic pathways, enhancing energy generation for metabolism, compared to the commercial effective bacterial agent. This paper provides both theoretical and practical evidence for the improvement of biochemical processor of FW with the personalized MCM, which has promising application prospects and economic value.},
}
@article {pmid39026261,
year = {2024},
author = {Lee, M and Kaul, A and Ward, JM and Zhu, Q and Richards, M and Wang, Z and González, A and Parks, CG and Beane Freeman, LE and Umbach, DM and Motsinger-Reif, AA and Knight, R and London, SJ},
title = {House dust metagenome and pulmonary function in a US farming population.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {129},
pmid = {39026261},
issn = {2049-2618},
support = {Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-CP010119B/CA/NCI NIH HHS/United States ; },
mesh = {*Dust/analysis ; Humans ; *Metagenome ; Female ; Male ; United States ; *Microbiota/genetics ; Middle Aged ; Lung/microbiology ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Forced Expiratory Volume ; Agriculture ; Respiratory Function Tests ; Vital Capacity ; Metagenomics/methods ; },
abstract = {BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.<br><br>RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.<br><br>CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.},
}
@article {pmid39026166,
year = {2024},
author = {Jing, Z and Zheng, W and Jianwen, S and Hong, S and Xiaojian, Y and Qiang, W and Yunfeng, Y and Xinyue, W and Shuwen, H and Feimin, Z},
title = {Gut microbes on the risk of advanced adenomas.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {264},
pmid = {39026166},
issn = {1471-2180},
support = {No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Adenoma/microbiology/virology ; *Feces/microbiology/virology ; *Colorectal Neoplasms/microbiology/virology ; Male ; Middle Aged ; Female ; Viruses/isolation &amp; purification/classification/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Aged ; Machine Learning ; },
abstract = {BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC.<br><br>OBJECTIVE: To analyze the characteristic microbes in AA.<br><br>METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze &#x3b1; diversity and &#x3b2; diversity. &#x3b1; diversity included box diagram, and &#x3b2; diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed.<br><br>RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively.<br><br>CONCLUSION: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.},
}
@article {pmid39024228,
year = {2024},
author = {Ravelo, AD and Ferm, P and Guo, Y and Omontese, BO and Morley, PS and Chen, C and Noyes, NR and Caixeta, LS},
title = {Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305674},
pmid = {39024228},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Milk/metabolism/microbiology ; *Lactation ; Phenotype ; Metabolome ; Microbiota ; Genomics/methods ; Metagenome ; Metabolomics/methods ; Multiomics ; },
abstract = {This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.},
}
@article {pmid39023095,
year = {2024},
author = {Zhang, P and Ma, S and Guo, R and Li, L and Guo, X and Chang, D and Li, S and Zhang, H and Fu, C and Yang, L and Zhang, Y and Jiang, J and Wang, T and Wang, J and Shi, H},
title = {Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29802},
doi = {10.1002/jmv.29802},
pmid = {39023095},
issn = {1096-9071},
mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology ; *Virome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Feces/virology/microbiology ; Viruses/classification/genetics/isolation &amp; purification ; Adult ; Male ; Female ; Middle Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.},
}
@article {pmid39022885,
year = {2024},
author = {Piontek, J and Hassenrück, C and Zäncker, B and Jürgens, K},
title = {Environmental control and metabolic strategies of organic-matter-responsive bacterioplankton in the Weddell Sea (Antarctica).},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16675},
doi = {10.1111/1462-2920.16675},
pmid = {39022885},
issn = {1462-2920},
support = {PI 784/3-1//Deutsche Forschungsgemeinschaft/ ; PI 784/4-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seawater/microbiology ; Antarctic Regions ; *Gammaproteobacteria/metabolism/genetics ; *Phytoplankton/metabolism/genetics ; Carbon/metabolism ; Microbiota ; Plankton/metabolism/genetics/growth &amp; development ; Metagenome ; Ecosystem ; Bacteroidetes/genetics/metabolism/growth &amp; development ; Temperature ; },
abstract = {Heterotrophic microbial communities play a significant role in driving carbon fluxes in marine ecosystems. Despite their importance, these communities remain understudied in remote polar oceans, which are known for their substantial contribution to the biological drawdown of atmospheric carbon dioxide. Our research focused on understanding the environmental factors and genetic makeup of key bacterial players involved in carbon remineralization in the Weddell Sea, including its coastal polynyas. Our experiments demonstrated that the combination of labile organic matter supply and temperature increase synergistically boosted bacterial growth. This suggests that, besides low seawater temperature, carbon limitation also hinders heterotrophic bacterial activity. Through the analysis of metagenome-assembled genomes, we discovered distinct genomic adaptation strategies in Bacteroidia and Gammaproteobacteria, both of which respond to organic matter. Both natural phytoplankton blooms and experimental addition of organic matter favoured Bacteroidia, which possess a large number of gene copies and a wide range of functional membrane transporters, glycoside hydrolases, and aminopeptidases. In contrast, the genomes of organic-matter-responsive Gammaproteobacteria were characterized by high densities of transcriptional regulators and transporters. Our findings suggest that bacterioplankton in the Weddell Sea, which respond to organic matter, employ metabolic strategies similar to those of their counterparts in temperate oceans. These strategies enable efficient growth at extremely low seawater temperatures, provided that organic carbon limitation is alleviated.},
}
@article {pmid39020289,
year = {2024},
author = {Pérez-Prieto, I and Vargas, E and Salas-Espejo, E and Lüll, K and Canha-Gouveia, A and Pérez, LA and Fontes, J and Salumets, A and Andreson, R and Aasmets, O and , and Whiteson, K and Org, E and Altmäe, S},
title = {Gut microbiome in endometriosis: a cohort study on 1000 individuals.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {294},
pmid = {39020289},
issn = {1741-7015},
mesh = {Humans ; *Endometriosis/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Case-Control Studies ; Estonia/epidemiology ; Cohort Studies ; Middle Aged ; Metagenomics ; Dysbiosis/microbiology ; Young Adult ; },
abstract = {BACKGROUND: Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most prevalent gynecological disorders. Although different theories have been proposed, its pathogenesis is not clear. Novel studies indicate that the gut microbiome may be involved in the etiology of endometriosis; nevertheless, the connection between microbes, their dysbiosis, and the development of endometriosis is understudied. This case-control study analyzed the gut microbiome in women with and without endometriosis to identify microbial targets involved in the disease.<br><br>METHODS: A subsample of 1000 women from the Estonian Microbiome cohort, including 136 women with endometriosis and 864 control women, was analyzed. Microbial composition was determined by shotgun metagenomics and microbial functional pathways were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Partitioning Around Medoids (PAM) algorithm was performed to cluster the microbial profile of the Estonian population. The alpha- and beta-diversity and differential abundance analyses were performed to assess the gut microbiome (species and KEGG orthologies (KO)) in both groups. Metagenomic reads were mapped to estrobolome-related enzymes' sequences to study potential microbiome-estrogen metabolism axis alterations in endometriosis.<br><br>RESULTS: Diversity analyses did not detect significant differences between women with and without endometriosis (alpha-diversity: all p-values&#x2009;>&#x2009;0.05; beta-diversity: PERMANOVA, both R [2]&#x2009;<&#x2009;0.0007, p-values&#x2009;>&#x2009;0.05). No differential species or pathways were detected after multiple testing adjustment (all FDR p-values&#x2009;>&#x2009;0.05). Sensitivity analysis excluding women at menopause (>&#x2009;50&#xa0;years) confirmed our results. Estrobolome-associated enzymes' sequence reads were not significantly different between groups (all FDR p-values&#x2009;>&#x2009;0.05).<br><br>CONCLUSIONS: Our findings do not provide enough evidence to support the existence of a gut microbiome-dependent mechanism directly implicated in the pathogenesis of endometriosis. To the best of our knowledge, this is the largest metagenome study on endometriosis conducted to date.},
}
@article {pmid39019914,
year = {2024},
author = {Dong, Y and Chen, R and Graham, EB and Yu, B and Bao, Y and Li, X and You, X and Feng, Y},
title = {Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6013},
pmid = {39019914},
issn = {2041-1723},
support = {41977045//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Salt Stress ; *Microbiota/genetics/drug effects ; *Climate Change ; Salinity ; Soil/chemistry ; Metagenomics ; Phylogeny ; Biological Evolution ; Genome, Bacterial ; Metagenome ; },
abstract = {With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.},
}
@article {pmid39019886,
year = {2024},
author = {Dhariwal, A and Rajar, P and Salvadori, G and Åmdal, HA and Berild, D and Saugstad, OD and Fugelseth, D and Greisen, G and Dahle, U and Haaland, K and Petersen, FC},
title = {Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6024},
pmid = {39019886},
issn = {2041-1723},
mesh = {Humans ; *Nasopharynx/microbiology ; *Infant, Premature ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Infant, Newborn ; Prospective Studies ; *Hospitalization ; Female ; Male ; Metagenomics/methods ; Infant ; Serratia marcescens/drug effects/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics/drug effects ; },
abstract = {Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.},
}
@article {pmid39017960,
year = {2024},
author = {Daddy Gaoh, S and Alusta, P and Lee, YJ and LiPuma, JJ and Hussong, D and Marasa, B and Ahn, Y},
title = {A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {273},
pmid = {39017960},
issn = {1432-0991},
mesh = {*Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Groundwater/microbiology ; Microbiota/genetics ; Pharmaceutical Preparations ; Metagenome ; Water Microbiology ; },
abstract = {In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome's taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436-557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.},
}
@article {pmid39016466,
year = {2024},
author = {Zhang, P and Shi, H and Guo, R and Li, L and Guo, X and Yang, H and Chang, D and Cheng, Y and Zhao, G and Li, S and Zhong, Q and Zhang, H and Zhao, P and Fu, C and Song, Y and Yang, L and Wang, Y and Zhang, Y and Jiang, J and Wang, T and Zhao, J and Li, Y and Wang, B and Chen, F and Zhao, H and Wang, Y and Wang, J and Ma, S},
title = {Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29809},
doi = {10.1002/jmv.29809},
pmid = {39016466},
issn = {1096-9071},
mesh = {Humans ; *Pancreatic Neoplasms/virology/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Metagenomics/methods ; *Feces/virology/microbiology ; Viruses/isolation &amp; purification/genetics/classification ; Metagenome ; Bacteria/isolation &amp; purification/classification/genetics ; Middle Aged ; Male ; Female ; Aged ; Case-Control Studies ; },
abstract = {Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.},
}
@article {pmid39015337,
year = {2024},
author = {Bashir, Z and Hugerth, LW and Krog, MC and Prast-Nielsen, S and Edfeldt, G and Boulund, F and Schacht, SR and Tetens, I and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Nielsen, HS},
title = {Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1324794},
pmid = {39015337},
issn = {2235-2988},
mesh = {Humans ; Female ; Adult ; Young Adult ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Adolescent ; *Depression/microbiology ; *Vagina/microbiology ; *Feces/microbiology ; *Stress, Psychological/microbiology ; Microbiota ; Denmark ; Healthy Volunteers ; Brain-Gut Axis/physiology ; Surveys and Questionnaires ; Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Despite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niches, such as the vaginal microbiota, are lacking in relation to mental health. This aim of this study was to investigate if the connections between the gut microbiome and mental health observed in populations with a clinical diagnosis of mental illness extend to healthy women experiencing stress and depressive symptoms. Additionally, this study examined the functional pathways of the gut microbiota according to the levels of psychological symptoms. Furthermore, the study aimed to explore potential correlations between the vaginal microbiome and mental health parameters in young women without psychiatric diagnoses.<br><br>METHODS: In this cross-sectional study, 160 healthy Danish women (aged 18-40 years) filled out questionnaires with validated scales measuring symptoms of stress and depression and frequency of dietary intake. Fecal and vaginal microbiota samples were collected at the beginning of the menstrual cycle and vaginal samples were also collected at cycle day 8-12 and 18-22. Shotgun metagenomic profiling of the gut and vaginal microbiome was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for functional profiling and 56 Gut Brain Modules were analyzed in the fecal samples.<br><br>RESULTS: The relative abundance in the gut of the genera Escherichia, Parabacteroides, and Shigella was higher in women with elevated depressive symptoms. Women with high perceived stress showed a tendency of increased abundance of Escherichia, Shigella, and Blautia. Amongst others, the potentially pathogenic genera, Escherichia and Shigella correlate with alterations in the neuroactive pathways such as the glutamatergic, GABAeric, dopaminergic, and Kynurenine pathways. Vaginosis symptoms were more prevalent in women reporting high levels of stress and depressive symptoms.<br><br>CONCLUSIONS: The findings of this study support the concept of a microbiota-associated effect on the neuroactive pathways even in healthy young women. This suggest, that targeting the gut microbiome could be a promising approach for future psychiatric interventions.},
}
@article {pmid39014300,
year = {2024},
author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C},
title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {241},
pmid = {39014300},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; },
abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.<br><br>RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.<br><br>CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.<br><br>AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .},
}
@article {pmid39012105,
year = {2024},
author = {Wu, W-C and Pan, Y-F and Zhou, W-D and Liao, Y-Q and Peng, M-W and Luo, G-Y and Xin, G-Y and Peng, Y-N and An, T and Li, B and Luo, H and Barrs, VR and Beatty, JA and Holmes, EC and Zhao, W and Shi, M and Shu, Y},
title = {Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043924},
doi = {10.1128/msphere.00439-24},
pmid = {39012105},
issn = {2379-5042},
abstract = {UNLABELLED: Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats.<br><br>IMPORTANCE: This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.},
}
@article {pmid39010229,
year = {2024},
author = {Chang, T and Gavelis, GS and Brown, JM and Stepanauskas, R},
title = {Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {126},
pmid = {39010229},
issn = {2049-2618},
support = {827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Plankton/genetics/classification/microbiology ; Phylogeny ; Seawater/microbiology ; Chimerism ; Genome, Bacterial ; Metagenomics/methods ; Microbiota/genetics ; Genomics ; },
abstract = {BACKGROUND: Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment.<br><br>RESULTS: We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages.<br><br>CONCLUSIONS: Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.},
}
@article {pmid39009515,
year = {2024},
author = {Takeda, M and Doki, Y},
title = {[The Power of the Gut Microbiome: Exploring New Perspectives in Colorectal Cancer Therapy].},
journal = {Gan to kagaku ryoho. Cancer &amp; chemotherapy},
volume = {51},
number = {6},
pages = {608-612},
pmid = {39009515},
issn = {0385-0684},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Dysbiosis/microbiology ; },
abstract = {The gut microbiome is involved in host physiology, including nutrition, metabolism, and immunity. It was recently known that dysbiosis of the gut microbiome has been implicated in several human diseases such as inflammatory bowel disease. It is altered by environmental factors such as diet, habit and lifestyle and has been directly and indirectly linked to the development and progression of colorectal cancer(CRC). Fusobacterium(F.)nucleatum, which causes periodontal disease, has been shown to play an important role in the initiation and development of CRC, although not as clearly as Helicobacter(H.) pylori in gastric cancer. Therefore, gut bacteria hold promise as a potential therapeutic approach to prevent or treat CRC. Although its clinical usefulness has not yet been demonstrated, future research such as metagenomics may open new avenues for CRC treatment with gut bacteria. Here, we reviewed the role of the gut microbial community in the development, progression, and prevention of colorectal carcinogenesis.},
}
@article {pmid39008123,
year = {2024},
author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B},
title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {93},
pmid = {39008123},
issn = {1432-184X},
support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; },
abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.},
}
@article {pmid39007947,
year = {2024},
author = {Nilsen, M and Nygaard, UC and Brodin, P and Carlsen, KCL and Fredheim, C and Haugen, G and Hedlin, G and Jonassen, CM and Jonsmoen, ULA and Lakshmikanth, T and Nordlund, B and Olin, A and Rehbinder, EM and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Vettukattil, R and Rudi, K},
title = {Gut bacteria at 6 months of age are associated with immune cell status in 1-year-old children.},
journal = {Scandinavian journal of immunology},
volume = {99},
number = {4},
pages = {e13346},
doi = {10.1111/sji.13346},
pmid = {39007947},
issn = {1365-3083},
support = {//Arne Ingel's legat/ ; //Barnestifteslen at Oslo University Hospital/ ; //Forte/ ; //F&#xfc;rst Medical Laboratory, Oslo, Norway/ ; //Health and Rehabilitation Norway/ ; //Karolinska Institutet/ ; //Norges Forskningsr&#xe5;d/ ; //Norwegian Association of Asthma and Allergy/ ; //Norwegian Society of Dermatology and Venerology/ ; //Oslo University Hospital/ ; //Region Stockholm (ALF-project and individual grants)/ ; //Roche/ ; //SFO-V Karolinska Institutet/ ; //Swedish Asthma and Allergy Association's Research Foundation/ ; //Swedish Order of Freemasons Foundation Barnhuset/ ; //Swedish Research council/ ; //Sykehuset &#xd8;stfold/ ; //The Cancer- and Allergy Foundation/ ; //Delegation of the European Union to Norway, University of Oslo/ ; //The Foundation for Healthcare and Allergy Research in Sweden - V&#xe5;rdalstiftelsen/ ; //The Fridtjof Nansen Institute/ ; //The Hesselman foundation/ ; //The Initiative for Clinical Therapy Research/ ; //The King Gustaf V 80th Birthday Foundation/ ; //The Kloster foundation/ ; //The Konsul Th C Bergh's Foundation/ ; //The Magnus Bergwall foundation/ ; //The Pediatric Research Foundation at Astrid Lindgren Children's Hospital/ ; //The Samaritan Foundation for Pediatric research/ ; //The Sven Jerring Foundation/ ; //The Swedish Heart-Lung Foundation/ ; //The Swedish Society of Medicine/ ; //Thermo-Fisher Uppsala, Sweden/ ; //Universitetet i Oslo/ ; },
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Feces/microbiology ; Infant, Newborn ; Bacteria/immunology/classification ; Fatty Acids, Volatile/metabolism ; Metagenome ; Prospective Studies ; },
abstract = {Age-related gut bacterial changes during infancy have been widely studied, but it remains still unknown how these changes are associated with immune cell composition. This study's aim was to explore if the temporal development of gut bacteria during infancy prospectively affects immune cell composition. Faecal bacteria and short-chain fatty acids were analysed from 67 PreventADALL study participants at four timepoints (birth to 12 months) using reduced metagenome sequencing and gas chromatography. Immune cell frequencies wer