@article {pmid39438539,
year = {2024},
author = {Guo, J and Li, Z and Liu, X and Jin, Y and Sun, Y and Yuan, Z and Zhang, W and Wang, J and Zhang, M},
title = {Response of the gut microbiota to changes in the nutritional status of red deer during winter.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24961},
pmid = {39438539},
issn = {2045-2322},
support = {2572023AW20//National Key Fundamental Research Funds for the Central Universities, China/ ; 2572020BE02//National Key Fundamental Research Funds for the Central Universities, China/ ; QLKH [2023] 11//the Guizhou Forestry Administration Scientific Research Project/ ; 2023GZJB005//the Reward and Subsidy Fund Project of Guizhou Education University, Ministry of Science and Technology of the People's Republic of China and National Natural Science Foundation of China/ ; 32071512//the National Natural Science Foundation of China, NSFC/ ; 2023YFF1305000//National Key Research and Development Program of China: Migration and diffusion mechanism of wild animals and population control technology/ ; ZKKF2022179//the Opening Research Projects for the Think Tanks of Heilongjiang Provincial Universities/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome ; *Seasons ; *Nutritional Status ; Feces/microbiology ; Nitrogen/metabolism/analysis ; Creatinine ; },
abstract = {Unravelling abrupt alterations in the gut microbiota of wild species associated with nutritional stress is imperative but challenging for wildlife conservation. This study assessed the nutritional status of wild red deer during winter on the basis of changes in faecal nitrogen (FN) and urea nitrogen/creatinine (UN: C) levels and identified gut microbes associated with nutritional status via nutritional control experiments and metagenomic sequencing. The FN of wild red deer in winter 2022 was significantly lower than that in winter 2021 (p < 0.05, winter 2021: 1.37 ± 0.16% and winter 2022: 1.26 ± 0.22%), and the UN: C ratio increased (winter 2021: 2.19 ± 1.65 and winter 2022: 3.05 ± 3.50). Similar trends were found in late winter, which indicated greater nutritional pressure in winter (2022) and late winter. Compared with winter 2021, abundances of Ructibacterium and Butyrivibrio significantly increased, and Acetatifactor and Cuneatibacter significantly decreased during winter 2022 (p < 0.05). Compared with early winter, the cell growth and death pathways increased and lipid metabolism and its subpathway of secondary bile acid synthesis (ko00121) significantly decreased during late winter (p < 0.05), which was similar to the changes in malnourished experimental red deer. Abrupt alterations in the gut microbiota should receive increased attention when monitoring the nutritional health of wild ungulates. This study provides new insights and critical implications for the conservation of wild ungulate populations.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome
*Seasons
*Nutritional Status
Feces/microbiology
Nitrogen/metabolism/analysis
Creatinine

@article {pmid39438328,
year = {2024},
author = {Varghese, P and Kumar, K and Sarkar, P and Karmakar, S and Shukla, SP and Kumar, S and Bharti, VS and Paul, T and Kantal, D},
title = {Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {113},
number = {5},
pages = {59},
pmid = {39438328},
issn = {1432-0800},
support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Govt. of India/ ; },
mesh = {*Triclosan/toxicity ; *Geologic Sediments/microbiology/chemistry ; *Biodiversity ; *Water Pollutants, Chemical/analysis/toxicity ; *Bacteria/drug effects ; },
abstract = {Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3 mg/L (T1) and 6 mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3 mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6 mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6 mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.},
}

*Triclosan/toxicity
*Geologic Sediments/microbiology/chemistry
*Biodiversity
*Water Pollutants, Chemical/analysis/toxicity
*Bacteria/drug effects

@article {pmid39436609,
year = {2025},
author = {Singer, F and Kuhring, M and Renard, BY and Muth, T},
title = {Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2859},
number = {},
pages = {297-318},
pmid = {39436609},
issn = {1940-6029},
mesh = {*Proteogenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Proteomics/methods ; Software ; Databases, Protein ; Metagenomics/methods ; Algorithms ; Metagenome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Mass Spectrometry/methods ; Proteome/genetics ; },
abstract = {Microbial sample analysis has received growing attention within the last decade, driven by important findings in microbiome research and promising applications in the biotechnological field. Modern mass spectrometry-based methodology has been established in this context, providing sufficient sensitivity, resolution, dynamic range, and throughput to analyze the so-called metaproteome of complex microbial mixtures from clinical or environmental samples. While proteomic analyses were previously restricted to common model organisms, next-generation sequencing technologies nowadays allow for the rapid and cost-efficient characterization of whole metagenomes of microbial consortia and specific genomes from non-model organisms to which microbes contribute by significant amounts. This proteogenomic approach, meaning the combined application of genomic and proteomic methods, enables researchers to create a protein database that presents a tailored blueprint of the microbial sample under investigation. This contribution provides an overview of the computational challenges and opportunities in proteogenomics and metaproteomics as of January 2018. For practical application, we first showcase an integrative proteogenomic method that circumvents existing reference databases by creating sample-specific transcripts. The underlying algorithm uses a graph network approach that combines RNA-Seq and peptide information. As a second example, we provide a tutorial for a simulation tool that estimates the computational limits of detecting microbial non-model organisms. This method evaluates the potential influence of error-tolerant searches and proteogenomic approaches on databases of interest. Finally, we discuss recommendations for developing future strategies that may help overcome present limitations by combining the strengths of genome- and proteome-based methods and moving toward an integrated metaproteogenomics approach.},
}

*Proteogenomics/methods
*Microbiota/genetics
Computational Biology/methods
Proteomics/methods
Software
Databases, Protein
Metagenomics/methods
Algorithms
Metagenome
Humans
High-Throughput Nucleotide Sequencing/methods
Mass Spectrometry/methods
Proteome/genetics

@article {pmid39435818,
year = {2024},
author = {He, L and Yan, YT and Yuan, CY and Lin, QS and Yu, DT},
title = {Characteristics of soil viral communities in Cunninghamia lanceolata plantations with different stand ages.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {9},
pages = {2543-2551},
doi = {10.13287/j.1001-9332.202409.007},
pmid = {39435818},
issn = {1001-9332},
mesh = {*Soil Microbiology ; *Cunninghamia/growth & development/virology ; Soil/chemistry ; Viruses/classification/isolation & purification/genetics ; China ; Virome ; Phosphorus/analysis ; },
abstract = {We investigated the dynamics of soil viral community in Cunninghamia lanceolata plantations with different stand ages (8, 21, 27, and 40 years old) in a subtropical region. The viral metagenomics and bioinformatics analysis were used to analyze the compositional and functional differences of soil viral communities across different stand ages, and to explore the environmental driving factors. The results showed that tailed phages dominated soil viral community in subtropical C. lanceolata plantations, with the highest proportion of Siphoviridae (19.6%-39.5%). There was significant difference in soil viral community structure among different stand ages, with the main driving factors being electrical conductance and available phosphorus. The metabolic functional genes encoded by viruses exhibited higher relative abundance. The α-diversity of soil viral function in mature C. lanceolata plantations was higher than other stands. There were significant differences in soil viral functional structure among different stand ages, which were mainly driven by ammonium nitrogen. During the development of C. lanceolata plantations, auxiliary metabolic genes encoded by virus related to nitrogen and phosphorus may regulate the metabolism of host microorganisms, thereby potentially impacting biogeochemical cycling of these elements.},
}

*Soil Microbiology
*Cunninghamia/growth & development/virology
Soil/chemistry
Viruses/classification/isolation & purification/genetics
China
Virome
Phosphorus/analysis

@article {pmid39434799,
year = {2024},
author = {Ghabban, H and Albalawi, DA and Al-Otaibi, AS and Alshehri, D and Alenzi, AM and Alatawy, M and Alatawi, HA and Alnagar, DK and Bahieldin, A},
title = {Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18282},
pmid = {39434799},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Avicennia/microbiology ; Saudi Arabia ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Wetlands ; },
abstract = {Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.},
}

*Soil Microbiology
*Avicennia/microbiology
Saudi Arabia
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Rhizosphere
Wetlands

@article {pmid39434178,
year = {2024},
author = {van Gogh, M and Louwers, JM and Celli, A and Gräve, S and Viveen, MC and Bosch, S and de Boer, NKH and Verheijden, RJ and Suijkerbuijk, KPM and Brand, EC and Top, J and Oldenburg, B and de Zoete, MR},
title = {Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {211},
pmid = {39434178},
issn = {2049-2618},
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Immunoglobulin A/immunology ; *Bacteria/genetics/classification/immunology ; High-Throughput Nucleotide Sequencing/methods ; Inflammatory Bowel Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: The intestinal microbiota plays a significant role in maintaining systemic and intestinal homeostasis, but can also influence diseases such as inflammatory bowel disease (IBD) and cancer. Certain bacterial species within the intestinal tract can chronically activate the immune system, leading to low-grade intestinal inflammation. As a result, plasma cells produce high levels of secretory antigen-specific immunoglobulin A (IgA), which coats the immunostimulatory bacteria. This IgA immune response against intestinal bacteria may be associated with the maintenance of homeostasis and health, as well as disease. Unraveling this dichotomy and identifying the immunostimulatory bacteria is crucial for understanding the relationship between the intestinal microbiota and the immune system, and their role in health and disease. IgA-SEQ technology has successfully identified immunostimulatory, IgA-coated bacteria from fecal material. However, the original technology is time-consuming and has limited downstream applications. In this study, we aimed to develop a next-generation, high-throughput, magnet-based sorting approach (ng-IgA-SEQ) to overcome the limitations of the original IgA-SEQ protocol.

RESULTS: We show, in various settings of complexity ranging from simple bacterial mixtures to human fecal samples, that our magnetic 96-well plate-based ng-IgA-SEQ protocol is highly efficient at sorting and identifying IgA-coated bacteria in a high-throughput and time efficient manner. Furthermore, we performed a comparative analysis between different IgA-SEQ protocols, highlighting that the original FACS-based IgA-SEQ approach overlooks certain nuances of IgA-coated bacteria, due to the low yield of sorted bacteria. Additionally, magnetic-based ng-IgA-SEQ allows for novel downstream applications. Firstly, as a proof-of-concept, we performed metagenomic shotgun sequencing on 10 human fecal samples to identify IgA-coated bacterial strains and associated pathways and CAZymes. Secondly, we successfully isolated and cultured IgA-coated bacteria by performing the isolation protocol under anaerobic conditions.

CONCLUSIONS: Our magnetic 96-well plate-based high-throughput next-generation IgA-SEQ technology efficiently identifies a great number of IgA-coated bacteria from fecal samples. This paves the way for analyzing large cohorts as well as novel downstream applications, including shotgun metagenomic sequencing, culturomics, and various functional assays. These downstream applications are essential to unravel the role of immunostimulatory bacteria in health and disease. Video Abstract.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
*Metagenomics/methods
*Immunoglobulin A/immunology
*Bacteria/genetics/classification/immunology
High-Throughput Nucleotide Sequencing/methods
Inflammatory Bowel Diseases/microbiology/immunology

@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0088824},
doi = {10.1128/msystems.00888-24},
pmid = {39352141},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}

*Metagenome/genetics
*Genome, Viral/genetics
*Metagenomics/methods
*Viruses/genetics/classification/isolation & purification
Software
Virome/genetics
Computational Biology/methods
Molecular Sequence Annotation

@article {pmid39320101,
year = {2024},
author = {Xue, H and Wang, Y and Mei, C and Han, L and Lu, M and Li, X and Chen, T and Wang, F and Tang, X},
title = {Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP).},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0083924},
doi = {10.1128/msystems.00839-24},
pmid = {39320101},
issn = {2379-5077},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Male ; Case-Control Studies ; *Metabolome ; Humans ; *Lactose Intolerance/microbiology ; Rats ; Female ; Adult ; Fecal Microbiota Transplantation ; Rats, Sprague-Dawley ; Middle Aged ; },
abstract = {UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment.

IMPORTANCE: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.},
}

*Gastrointestinal Microbiome/physiology
Animals
Male
Case-Control Studies
*Metabolome
Humans
*Lactose Intolerance/microbiology
Rats
Female
Adult
Fecal Microbiota Transplantation
Rats, Sprague-Dawley
Middle Aged

@article {pmid39315779,
year = {2024},
author = {Rajeev, M and Jung, I and Kang, I and Cho, J-C},
title = {Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0078224},
doi = {10.1128/msystems.00782-24},
pmid = {39315779},
issn = {2379-5077},
support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (KIMST)/ ; NRF-2022R1A2C3008502,NRF-2018R1A5A1025077//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Aquaculture ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Archaea/genetics/metabolism/classification ; Metagenome ; Phylogeny ; Penaeidae/microbiology/genetics ; },
abstract = {UNLABELLED: Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.

IMPORTANCE: Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.},
}

*Aquaculture
*Metagenomics/methods
Animals
*Microbiota/genetics
Bacteria/genetics/metabolism/classification
Archaea/genetics/metabolism/classification
Metagenome
Phylogeny
Penaeidae/microbiology/genetics

@article {pmid39305897,
year = {2024},
author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M},
title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.},
journal = {Current biology : CB},
volume = {34},
number = {20},
pages = {4650-4661.e4},
doi = {10.1016/j.cub.2024.08.047},
pmid = {39305897},
issn = {1879-0445},
mesh = {*DNA, Ancient/analysis ; Animals ; *Archaeology ; Forests ; Sheep/genetics ; Microbiota/genetics ; Agriculture/history ; Geologic Sediments/analysis ; Europe ; },
abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."},
}

*DNA, Ancient/analysis
Animals
*Archaeology
Forests
Sheep/genetics
Microbiota/genetics
Agriculture/history
Geologic Sediments/analysis
Europe

@article {pmid39287376,
year = {2024},
author = {Bucher-Johannessen, C and Senthakumaran, T and Avershina, E and Birkeland, E and Hoff, G and Bemanian, V and Tunsjø, H and Rounge, TB},
title = {Species-level verification of Phascolarctobacterium association with colorectal cancer.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0073424},
doi = {10.1128/msystems.00734-24},
pmid = {39287376},
issn = {2379-5077},
support = {2020056//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 190179//Kreftforeningen (NCS)/ ; 198048//Kreftforeningen (NCS)/ ; 202401/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Norway/epidemiology ; Metagenome ; Middle Aged ; Adenoma/microbiology/genetics ; Aged ; },
abstract = {We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology
Male
Female
*RNA, Ribosomal, 16S/genetics
Gastrointestinal Microbiome/genetics
Norway/epidemiology
Metagenome
Middle Aged
Adenoma/microbiology/genetics
Aged

@article {pmid39287374,
year = {2024},
author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A},
title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0058524},
doi = {10.1128/msystems.00585-24},
pmid = {39287374},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics & numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics & numerical data ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Young Adult ; },
abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.

IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Urbanization
Male
Female
Kazakhstan/epidemiology
*Diet
Adult
Rural Population/statistics & numerical data
Middle Aged
Prospective Studies
RNA, Ribosomal, 16S/genetics
Urban Population/statistics & numerical data
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Young Adult

@article {pmid39283083,
year = {2024},
author = {Brennan, C and Belda-Ferre, P and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Ackermann, G and Allaband, C and Ambre, M and Boyer, T and Bryant, M and Cantrell, K and Gonzalez, A and McDonald, D and Salido, RA and Song, SJ and Wright, G and Dorrestein, PC and Knight, R},
title = {Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0098524},
doi = {10.1128/msystems.00985-24},
pmid = {39283083},
issn = {2379-5077},
support = {U19AG063744//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Microbiota/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; },
abstract = {UNLABELLED: Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers of samples poses many challenges, with cross-contamination being the biggest obstacle. Contamination complicates analysis and results in sample loss, leading to higher costs and constraints on mixed sample type study designs. While many researchers opt for 96-well plates for their workflows, these plates present a significant issue: the shared seal and weak separation between wells leads to well-to-well contamination. To address this concern, we propose an innovative high-throughput approach, termed as the Matrix method, which employs barcoded Matrix Tubes for sample acquisition. This method is complemented by a paired nucleic acid and metabolite extraction, utilizing 95% (vol/vol) ethanol to stabilize microbial communities and as a solvent for extracting metabolites. Comparative analysis between conventional 96-well plate extractions and the Matrix method, measuring 16S rRNA gene levels via quantitative polymerase chain reaction, demonstrates a notable decrease in well-to-well contamination with the Matrix method. Metagenomics, 16S rRNA gene amplicon sequencing (16S), and untargeted metabolomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed that the Matrix method recovers reproducible microbial and metabolite compositions that can distinguish between subjects. This advancement is critical for large-scale study design as it minimizes well-to-well contamination and technical variation, shortens processing times, and integrates with automated infrastructure for enhancing sample randomization and metadata generation.

IMPORTANCE: Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.},
}

*Microbiota/genetics
Humans
*RNA, Ribosomal, 16S/genetics
Specimen Handling/methods

@article {pmid39254351,
year = {2024},
author = {Wasmund, K and Singleton, C and Dahl Dueholm, MK and Wagner, M and Nielsen, PH},
title = {The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0030124},
doi = {10.1128/msystems.00301-24},
pmid = {39254351},
issn = {2379-5077},
mesh = {*Sewage/microbiology ; *Proteome/metabolism/analysis ; Bacterial Proteins/genetics/metabolism ; Nutrients/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; Metagenome ; Microbiota/genetics ; },
abstract = {In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.},
}

*Sewage/microbiology
*Proteome/metabolism/analysis
Bacterial Proteins/genetics/metabolism
Nutrients/metabolism/analysis
Bacteria/metabolism/genetics/classification
Metagenome
Microbiota/genetics

@article {pmid39254336,
year = {2024},
author = {Jung, D and Park, S and Kurban, D and Dufour, S and Ronholm, J},
title = {The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0036224},
doi = {10.1128/msystems.00362-24},
pmid = {39254336},
issn = {2379-5077},
support = {Dairy Research Cluster 3//Dairy Farmers of Canada (DFC)/ ; },
mesh = {Animals ; Female ; *Milk/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; *Escherichia coli/isolation & purification/genetics ; *Aerococcus/isolation & purification/genetics ; *Escherichia coli Infections/microbiology/veterinary ; *Staphylococcus/isolation & purification/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation.IMPORTANCEIn this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.},
}

Animals
Female
*Milk/microbiology
Cattle
*Mastitis, Bovine/microbiology
*Escherichia coli/isolation & purification/genetics
*Aerococcus/isolation & purification/genetics
*Escherichia coli Infections/microbiology/veterinary
*Staphylococcus/isolation & purification/genetics
Microbiota/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid39240096,
year = {2024},
author = {Ruiz-Perez, D and Gimon, I and Sazal, M and Mathee, K and Narasimhan, G},
title = {Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0130323},
doi = {10.1128/msystems.01303-23},
pmid = {39240096},
issn = {2379-5077},
support = {1R15AI128714-01//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; Dissertation Year Fellowship//University Graduate School, Florida International University (UGS)/ ; },
mesh = {Humans ; *Algorithms ; Microbiota/genetics ; Longitudinal Studies ; Gastrointestinal Microbiome/genetics ; Metabolomics ; Computational Biology/methods ; Multiomics ; },
abstract = {UNLABELLED: A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novel unrolling and de-confounding techniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. The unrolling process helps identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; the de-confounding process identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery, and network inference algorithms were applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.

IMPORTANCE: We have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICA introduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the inflammatory bowel disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work. From this dataset, we generated various subsets, encompassing different combinations of metagenomics, metabolomics, and metatranscriptomics datasets. Using these multi-omics datasets, we demonstrate how the unrolling process aids in the identification of putative intermediaries (genes and/or metabolites) to explain the interactions between microbes. Additionally, the de-confounding process identifies potential common causes that may give rise to spurious relationships to be inferred. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.},
}

Humans
*Algorithms
Microbiota/genetics
Longitudinal Studies
Gastrointestinal Microbiome/genetics
Metabolomics
Computational Biology/methods
Multiomics

@article {pmid39159427,
year = {2024},
author = {Yagi, K and Ethridge, AD and Falkowski, NR and Huang, YJ and Elesela, S and Huffnagle, GB and Lukacs, NW and Fonseca, W and Asai, N},
title = {Microbiome modifications by steroids during viral exacerbation of asthma and in healthy mice.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {327},
number = {5},
pages = {L646-L660},
doi = {10.1152/ajplung.00040.2024},
pmid = {39159427},
issn = {1522-1504},
support = {AI138348//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; HL150682//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; AI089473//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; *Asthma/virology/microbiology/drug therapy ; *Respiratory Syncytial Virus Infections/virology/drug therapy/microbiology/immunology ; *Fluticasone/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Lung/virology/microbiology/metabolism/drug effects ; Female ; Mice, Inbred BALB C ; Microbiota/drug effects ; Respiratory Syncytial Viruses/drug effects ; },
abstract = {In the present studies, the assessment of how viral exacerbation of asthmatic responses with and without pulmonary steroid treatment alters the microbiome in conjunction with immune responses presents striking data. The overall findings identify that although steroid treatment of allergic animals diminished the severity of the respiratory syncytial virus (RSV)-induced exacerbation of airway function and mucus hypersecretion, there were local increases in IL-17 expression. Analysis of the lung and gut microbiome suggested that there are differences in RSV exacerbation that are further altered by fluticasone (FLUT) treatment. Using metagenomic inference software, PICRUSt2, we were able to predict that the metabolite profile produced by the changed gut microbiome was significantly different with multiple metabolic pathways and associated with specific treatments with or without FLUT. Importantly, measuring plasma metabolites in an unbiased manner, our data indicate that there are significant changes associated with chronic allergen exposure, RSV exacerbation, and FLUT treatment that are reflective of responses to the disease and treatment. In addition, the changes in metabolites appeared to have contributions from both host and microbial pathways. To understand if airway steroids on their own altered lung and gut microbiome along with host responses to RSV infection, naïve animals were treated with lung FLUT before RSV infection. The naïve animals treated with FLUT before RSV infection demonstrated enhanced disease that corresponded to an altered microbiome and the related PICRUSt2 metagenomic inference analysis. Altogether, these findings set the foundation for identifying important correlations of severe viral exacerbated allergic disease with microbiome changes and the relationship of host metabolome with a potential for early life pulmonary steroid influence on subsequent viral-induced disease.NEW & NOTEWORTHY These studies outline a novel finding that airway treatment with fluticasone, a commonly used inhaled steroid, has significant effects on not only the local lung environment but also on the mucosal microbiome, which may have significant disease implications. The findings further provide data to support that pulmonary viral exacerbations of asthma with or without steroid treatment alter the lung and gut microbiome, which have an impact on the circulating metabolome that likely alters the trajectory of disease progression.},
}

Animals
*Asthma/virology/microbiology/drug therapy
*Respiratory Syncytial Virus Infections/virology/drug therapy/microbiology/immunology
*Fluticasone/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
Lung/virology/microbiology/metabolism/drug effects
Female
Mice, Inbred BALB C
Microbiota/drug effects
Respiratory Syncytial Viruses/drug effects

@article {pmid38808521,
year = {2024},
author = {Park, JS and Kim, E and Kwon, SJ and Heo, JS and Ahn, KH},
title = {Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study.},
journal = {Journal of periodontal research},
volume = {59},
number = {5},
pages = {939-950},
doi = {10.1111/jre.13292},
pmid = {38808521},
issn = {1600-0765},
support = {//Korea University Medicine/ ; //Korea University Anam Hospital/ ; //National Research Foundation of Korea/ ; //Korea University/ ; //Ministry of Trade, Industry and Energy/ ; },
mesh = {Humans ; Female ; *Premature Birth/microbiology ; Adult ; *Microbiota ; Pregnancy ; *Term Birth ; Prospective Studies ; *Gingiva/microbiology ; Periodontal Index ; Periodontitis/microbiology ; Dental Plaque/microbiology ; RNA, Ribosomal, 16S/analysis ; },
abstract = {AIM: Periodontitis is a potential risk factor for preterm birth (PTB) in women; however, the causal relationship or the exact mechanism remain unknown. This study aimed to compare the oral microbiome features of mothers with full-term birth (FTB) with those who had preterm delivery.

METHODS: This study prospectively enrolled 60 women (30 mothers with PTB and 30 mothers with FTB), and subgingival plaque samples were collected and analysed by metagenomic 16S rDNA sequencing. Clinical measurements, including periodontal probing depth, clinical attachment level, modified gingival index (mGI) and plaque index, were performed to determine the periodontal state of the participants. Medical and obstetric data were collected as well.

RESULTS: Among the periodontal measurements, mGI score, reflecting the level of gingival inflammation, exhibited a statistically significant association with PTB (adjusted odds ratio 2.705, 95% confidence interval 1.074-6.811, p = .035). When subgroup analysis was conducted based on mean mGI scores (mGI ≥ 2, high inflammation [HI] versus mGI < 2, low inflammation [LI]), microbiome analysis revealed clear distinctions in microbial compositions between PTB and FTB mothers in both the HI and LI groups. Especially in the HI group, alpha diversity exhibited a decreasing trend in PTB mothers compared to FTB mothers. Beta diversity also revealed significant differences between the two groups. In Linear Discriminant Analysis Effect Size analysis, certain anaerobic taxa, including the genera Spirochaetes, Treponema and Porphyromonas, were relatively abundant in the FTB/HI group, whereas the PTB/HI group showed a high abundance of the order Actinomycetales. Network analysis showed that the FTB/HI had relatively stronger connectivity in microbial composition than the PTB/HI group. Dysbiosis ratio of plaque microbiome, in terms of periodontitis, was significantly lower in PTB/HI group compared to FTB/HI group.

CONCLUSION: The compositions of maternal subgingival microbiomes differed between PTB and FTB mothers in both the high and low levels of gingival inflammation groups. In the presence of high level of gingival inflammation, dysbiosis in plaque microbiome, in terms of periodontitis, was decreased in PTB mothers compared to FTB mothers.},
}

Humans
Female
*Premature Birth/microbiology
Adult
*Microbiota
Pregnancy
*Term Birth
Prospective Studies
*Gingiva/microbiology
Periodontal Index
Periodontitis/microbiology
Dental Plaque/microbiology
RNA, Ribosomal, 16S/analysis

@article {pmid39434181,
year = {2024},
author = {Chen, CZ and Li, P and Liu, L and Sun, YJ and Ju, WM and Li, ZH},
title = {Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {209},
pmid = {39434181},
issn = {2049-2618},
support = {42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; },
abstract = {BACKGROUND: The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.

RESULTS: The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.

CONCLUSIONS: This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.},
}

@article {pmid39432783,
year = {2024},
author = {Oguro-Igashira, E and Murakami, M and Mori, R and Kuwahara, R and Kihara, T and Kohara, M and Fujiwara, M and Motooka, D and Okuzaki, D and Arase, M and Toyota, H and Peng, S and Ogino, T and Kitabatake, Y and Morii, E and Hirota, S and Ikeuchi, H and Umemoto, E and Kumanogoh, A and Takeda, K},
title = {The pyruvate-GPR31 axis promotes transepithelial dendrite formation in human intestinal dendritic cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {44},
pages = {e2318767121},
doi = {10.1073/pnas.2318767121},
pmid = {39432783},
issn = {1091-6490},
support = {JP21H050430//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K07895//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21gm1010004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJSP213//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; J178501002//BD Biosciences (Becton Dickenson Biosciences)/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism ; *Dendritic Cells/metabolism ; *Pyruvic Acid/metabolism ; Intestinal Mucosa/metabolism/cytology ; Dendrites/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Induced Pluripotent Stem Cells/metabolism/cytology ; Organoids/metabolism ; Intestines/cytology ; },
abstract = {The intestinal lumen is rich in gut microbial metabolites that serve as signaling molecules for gut immune cells. G-protein-coupled receptors (GPCRs) sense metabolites and can act as key mediators that translate gut luminal signals into host immune responses. However, the impacts of gut microbe-GPCR interactions on human physiology have not been fully elucidated. Here, we show that GPR31, which is activated by the gut bacterial metabolite pyruvate, is specifically expressed on type 1 conventional dendritic cells (cDC1s) in the lamina propria of the human intestine. Using human induced pluripotent stem cell-derived cDC1s and a monolayer human gut organoid coculture system, we show that cDC1s extend their dendrites toward pyruvate on the luminal side, forming transepithelial dendrites (TED). Accordingly, GPR31 activation via pyruvate enhances the fundamental function of cDC1 by allowing efficient uptake of gut luminal antigens, such as dietary compounds and bacterial particles through TED formation. Our results highlight the role of GPCRs in tuning the human gut immune system according to local metabolic cues.},
}

Humans
*Receptors, G-Protein-Coupled/metabolism
*Dendritic Cells/metabolism
*Pyruvic Acid/metabolism
Intestinal Mucosa/metabolism/cytology
Dendrites/metabolism
Gastrointestinal Microbiome
Signal Transduction
Induced Pluripotent Stem Cells/metabolism/cytology
Organoids/metabolism
Intestines/cytology

@article {pmid39432094,
year = {2024},
author = {Shafana Farveen, M and Narayanan, R},
title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.},
journal = {Archives of microbiology},
volume = {206},
number = {11},
pages = {441},
pmid = {39432094},
issn = {1432-072X},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; },
abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.},
}

*Biodegradation, Environmental
*Plastics/metabolism
*Microbiota
Bacteria/metabolism/genetics/classification
Proteomics
Genomics
Microbial Consortia

@article {pmid39431789,
year = {2024},
author = {Bickerstaff, JRM and Walsh, T and Court, L and Pandey, G and Ireland, K and Cousins, D and Caron, V and Wallenius, T and Slipinski, A and Rane, R and Escalona, HE},
title = {Chromosome structural rearrangements in invasive haplodiploid ambrosia beetles revealed by the genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae226},
pmid = {39431789},
issn = {1759-6653},
abstract = {Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed E. similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance and management. Using a combination of long and short read sequencing platforms we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome level genomes for these species. Comparative macro-synteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.},
}

@article {pmid39431768,
year = {2024},
author = {Tutagata, J and Pocquet, N and Trouche, B and Reveillaud, J},
title = {Dissection of Mosquito Ovaries, Midgut, and Salivary Glands for Microbiome Analyses at the Organ Level.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {212},
pages = {},
doi = {10.3791/67128},
pmid = {39431768},
issn = {1940-087X},
mesh = {Animals ; Female ; *Salivary Glands/microbiology ; *Microbiota/physiology ; *Ovary/microbiology ; Dissection/methods ; Culicidae/microbiology ; },
abstract = {The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.},
}

Animals
Female
*Salivary Glands/microbiology
*Microbiota/physiology
*Ovary/microbiology
Dissection/methods
Culicidae/microbiology

@article {pmid39431056,
year = {2024},
author = {Han, L and Hu, C and Du, Z and Yu, H and Du, Y and Li, L and Li, F and Wang, Y and Gao, X and Sun, X and Zhang, Z and Qin, Y},
title = {Association of glycerolipid metabolism with gut microbiota disturbances in a hamster model of high-fat diet-induced hyperlipidemia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1439744},
pmid = {39431056},
issn = {2235-2988},
mesh = {Animals ; *Hyperlipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Cricetinae ; *Disease Models, Animal ; *Liver/metabolism ; Male ; *Lipid Metabolism ; *Feces/microbiology ; Metabolomics ; Bacteria/classification/isolation & purification/metabolism/genetics ; Metagenomics ; Lipids/blood ; },
abstract = {BACKGROUND: High-fat diet (HFD)-induced hyperlipidemia, which is associated with gut microbiota disturbances, remains a major public health challenge. Glycerolipid metabolism is responsible for lipid synthesis and is thus involved in the development of hyperlipidemia. However, possible association between the HFD-modulated gut microbiome and the glycerolipid metabolism pathway remains unclear.

METHODS: Hamsters were fed a HFD for 4 weeks to establish a hyperlipidemia model. Fecal, plasma and liver samples collected from hamsters fed a HFD or a normal chow diet (NCD) were used for integrative metagenomic and untargeted metabolomic analyses to explore changes in the composition and functions of the gut microbiota, and relevant metabolites. Spearman rank correlation analysis was used to explore correlations between gut microbes and circulating glycerolipid metabolites, gut microbes and lipids, and circulating glycerolipid metabolites and lipids.

RESULTS: The gut microbial composition of HFD hamsters showed significant alterations at the phylum, genus, and species levels that were skewed toward metabolic disorders compared with that of NCD hamsters. Functional characterization by KEGG analysis identified enrichment of the glycerolipid metabolism pathway in the gut microbiome of HFD hamsters. Plasma and liver metabolomics further indicated the upregulation and enrichment of glycerolipid metabolites in HFD hamsters. The Faecalibaculum, Allobaculum, and Eubacterium genera were positively correlated with plasma glycerolipid metabolites and lipid indices.

CONCLUSION: The findings of this study suggest an association between glycerolipid metabolism and the HFD-modulated gut microbiome that is involved in the development of hyperlipidemia.},
}

Animals
*Hyperlipidemias/metabolism/microbiology
*Gastrointestinal Microbiome
*Diet, High-Fat/adverse effects
Cricetinae
*Disease Models, Animal
*Liver/metabolism
Male
*Lipid Metabolism
*Feces/microbiology
Metabolomics
Bacteria/classification/isolation & purification/metabolism/genetics
Metagenomics
Lipids/blood

@article {pmid39428758,
year = {2024},
author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J},
title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2414975},
doi = {10.1080/19490976.2024.2414975},
pmid = {39428758},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; },
abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.

RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.

CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Female
Metagenomics
Microbial Consortia
Metagenome
Infant, Newborn
Cohort Studies
Cystic Fibrosis/microbiology

@article {pmid39218360,
year = {2024},
author = {Park, DG and Kang, W and Shin, IJ and Chalita, M and Oh, HS and Hyun, DW and Kim, H and Chun, J and An, YS and Lee, EJ and Yoon, JH},
title = {Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease.},
journal = {Neurobiology of disease},
volume = {201},
number = {},
pages = {106655},
doi = {10.1016/j.nbd.2024.106655},
pmid = {39218360},
issn = {1095-953X},
mesh = {Humans ; *Parkinson Disease/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Aged ; Middle Aged ; *Dysbiosis/microbiology ; REM Sleep Behavior Disorder/microbiology ; Brain/metabolism/microbiology ; },
abstract = {BACKGROUND: This study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes.

METHODS: In this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls.

RESULTS: Significant differences were found in the gut microbiome of body-first PD patients (n = 15) compared to both brain-first PD patients (n = 9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently.

CONCLUSIONS: Our findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.},
}

Humans
*Parkinson Disease/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Male
Female
Cross-Sectional Studies
Aged
Middle Aged
*Dysbiosis/microbiology
REM Sleep Behavior Disorder/microbiology
Brain/metabolism/microbiology

@article {pmid39426981,
year = {2024},
author = {Lu, C and Liu, D and Wu, Q and Zeng, J and Xiong, Y and Luo, T},
title = {EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {108},
pmid = {39426981},
issn = {2055-5008},
support = {2023NSFSC1631//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2023YFS0116//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2022YFS0604//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; Q22066//Education Department of Sichuan Province/ ; },
mesh = {Animals ; *Atherosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Mice ; *Receptor, EphA2/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Humans ; Disease Models, Animal ; Plaque, Atherosclerotic/etiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dysbiosis ; },
abstract = {Coronary artery disease (CAD), a critical condition resulting from systemic inflammation, metabolic dysfunction, and gut microbiota dysbiosis, poses a global public health challenge. ALW-II-41-27, a specific inhibitor of the EphA2 receptor, has shown anti-inflammatory prosperities. However, the impact of ALW-II-41-27 on atherosclerosis has not been elucidated. This study aimed to examine the roles of pharmacologically inhibiting EphA2 and the underlying mechanism in ameliorating atherosclerosis. ALW-II-41-27 was administered to apoE[-/-] mice fed a high-fat diet via intraperitoneal injection. We first discovered that ALW-II-41-27 led to a significant reduction in atherosclerotic plaques, evidenced by reduced lipid and macrophage accumulation, alongside an increase in collagen and smooth muscle cell content. ALW-II-41-27 also significantly lowered plasma and hepatic cholesterol levels, as well as the colonic inflammation. Furthermore, gut microbiota was analyzed by metagenomics and plasma metabolites by untargeted metabolomics. ALW-II-41-27-treated mice enriched Enterococcus, Akkermansia, Eggerthella and Lactobaccilus, accompanied by enhanced secondary bile acids production. To explore the causal link between ALW-II-41-27-associated gut microbiota and atherosclerosis, fecal microbiota transplantation was employed. Mice that received ALW-II-41-27-treated mouse feces exhibited the attenuated atherosclerotic plaque. In clinical, lower plasma DCA and HDCA levels were determined in CAD patients using quantitative metabolomics and exhibited a negative correlation with higher monocytes EphA2 expression. Our findings underscore the potential of ALW-II-41-27 as a novel therapeutic agent for atherosclerosis, highlighting its capacity to modulate gut microbiota composition and bile acid metabolism, thereby offering a promising avenue for CAD.},
}

Animals
*Atherosclerosis/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
*Bile Acids and Salts/metabolism
Mice
*Receptor, EphA2/metabolism
*Diet, High-Fat/adverse effects
Male
Humans
Disease Models, Animal
Plaque, Atherosclerotic/etiology
Mice, Inbred C57BL
Bacteria/classification/isolation & purification/genetics/metabolism
Dysbiosis

@article {pmid39425237,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {206},
pmid = {39425237},
issn = {2049-2618},
support = {F30AI169759/NH/NIH HHS/United States ; T32AI055397/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Adult ; Infant ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Age Factors ; Child, Preschool ; Healthy Volunteers ; Metagenomics/methods ; Respiratory System/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.},
}

Humans
*Microbiota
*Mouth/microbiology
Adult
Infant
Female
*Bacteria/classification/genetics/isolation & purification
Male
Age Factors
Child, Preschool
Healthy Volunteers
Metagenomics/methods
Respiratory System/microbiology
Metagenome

@article {pmid39425038,
year = {2024},
author = {Woldeyohannis, NN and Desta, AF},
title = {Metagenome-based microbial community analysis of urine-derived fertilizer.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {418},
pmid = {39425038},
issn = {1471-2180},
mesh = {Humans ; *Fertilizers/analysis ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Struvite ; *Metagenome ; Microbiota/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.},
}

Humans
*Fertilizers/analysis
*Urine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Struvite
*Metagenome
Microbiota/genetics
Metagenomics/methods
DNA, Bacterial/genetics
Phylogeny

@article {pmid39207108,
year = {2024},
author = {Crouch, AL and Monsey, L and Rambeau, M and Ramos, C and Yracheta, JM and Anderson, MZ},
title = {Metagenomic discovery of microbial eukaryotes in stool microbiomes.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0206324},
pmid = {39207108},
issn = {2150-7511},
support = {//Ohio State University (OSU)/ ; 2046863//National Science Foundation (NSF)/ ; //Chan Zuckerberg Initiative (CZI)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Feces/microbiology ; *Eukaryota/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Fungi/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Microbiota/genetics ; },
abstract = {Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.},
}

Humans
*Metagenomics/methods
*Feces/microbiology
*Eukaryota/genetics/classification/isolation & purification
Gastrointestinal Microbiome/genetics
Metagenome
Fungi/genetics/classification/isolation & purification
Sequence Analysis, DNA/methods
Microbiota/genetics

@article {pmid39192744,
year = {2024},
author = {Metcalfe-Roach, A and Cirstea, MS and Yu, AC and Ramay, HR and Coker, O and Boroomand, S and Kharazyan, F and Martino, D and Sycuro, LK and Appel-Cresswell, S and Finlay, BB},
title = {Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {39},
number = {10},
pages = {1740-1751},
doi = {10.1002/mds.29959},
pmid = {39192744},
issn = {1531-8257},
support = {GR008160//Pacific Parkinson's Research Institute/ ; FDN-159935/CAPMC/CIHR/Canada ; PPG-2020-0000000052//Parkinson Canada/ ; FDN-159935/CAPMC/CIHR/Canada ; },
mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; Aged ; Middle Aged ; *Metagenomics/methods ; *Feces/microbiology ; Disease Progression ; },
abstract = {BACKGROUND: Parkinson's disease (PD) has been consistently linked to alterations within the gut microbiome.

OBJECTIVE: Our goal was to identify microbial features associated with PD incidence and progression.

METHODS: Metagenomic sequencing was used to characterize taxonomic and functional changes to the PD microbiome and to explore their relation to bacterial metabolites and disease progression. Motor and non-motor symptoms were tracked using Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and levodopa equivalent dose across ≤5 yearly study visits. Stool samples were collected at baseline for metagenomic sequencing (176 PD, 100 controls).

RESULTS: PD-derived stool samples had reduced intermicrobial connectivity and seven differentially abundant species compared to controls. A suite of bacterial functions differed between PD and controls, including depletion of carbohydrate degradation pathways and enrichment of ribosomal genes. Faecalibacterium prausnitzii-specific reads contributed significantly to more than half of all differentially abundant functional terms. A subset of disease-associated functional terms correlated with faster progression of MDS-UPDRS part IV and separated those with slow and fast progression with moderate accuracy within a random forest model (area under curve = 0.70). Most PD-associated microbial trends were stronger in those with symmetric motor symptoms.

CONCLUSION: We provide further evidence that the PD microbiome is characterized by reduced intermicrobial communication and a shift to proteolytic metabolism in lieu of short-chain fatty acid production, and suggest that these microbial alterations may be relevant to disease progression. We also describe how our results support the existence of gut-first versus brain-first PD subtypes. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}

Humans
*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Male
Female
Aged
Middle Aged
*Metagenomics/methods
*Feces/microbiology
Disease Progression

@article {pmid38879123,
year = {2024},
author = {Jiang, X and Wang, X and Zhang, M and Yu, L and He, J and Wu, S and Yan, J and Zheng, Y and Zhou, Y and Chen, Y},
title = {Associations between specific dietary patterns, gut microbiome composition, and incident subthreshold depression in Chinese young adults.},
journal = {Journal of advanced research},
volume = {65},
number = {},
pages = {183-195},
doi = {10.1016/j.jare.2024.05.030},
pmid = {38879123},
issn = {2090-1224},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Young Adult ; Adult ; *Depression/microbiology ; Cross-Sectional Studies ; Adolescent ; *Feeding Behavior ; *Diet/methods ; China ; *Feces/microbiology ; Incidence ; Dietary Patterns ; East Asian People ; },
abstract = {INTRODUCTION: The interplay between influential factors and the incidence of subthreshold depression (SD) in young adults remains poorly understood.

OBJECTIVES: This study sought to understand the dietary habits, gut microbiota composition, etc. among individuals with SD in young adults and to investigate their association with SD occurrence.

METHODS: Employing a cross-sectional approach, 178 individuals with SD, aged 18-32 years, were matched with 114 healthy counterparts. SD status was evaluated using the Zung Self-rating Depression Scale (SDS), Zung Self-rating Anxiety Scale (SAS), Beck Depression Inventory 2nd version (BDI-II), the 17-item Hamilton Rating Scales of Depression (HAMD-17), and Pittsburgh Sleep Quality Index (PSQI). Metagenomic sequencing was utilized to identify fecal microbial profiles. Dietary patterns were discerned via factor analysis of a 25-item food frequency questionnaire (FFQ). Logistic regression analysis and mediation analysis were performed to explore the potential links between gut microbiota, dietary patterns, and incident SD.

RESULTS: Data on dietary habits were available for 292 participants (mean [SD] age, 22.1 [2.9] years; 216 [73.9 %] female). Logistic regression analysis revealed that dietary patterns Ⅰ (odds ratio [OR], 0.34; 95 % CI, 0.15-0.75) and IV (OR, 0.39; 95 % CI, 0.17-0.86 and OR, 0.39; 95 % CI, 0.18-0.84) were associated with reduced risk of SD. Distinct microbial profiles were observed in young adults with SD, marked by increased microbial diversity and taxonomic alterations. Moreover, mediation analysis suggested Veillonella atypica as a potential mediator linking SDS or BDI-II scores with a healthy dietary pattern rich in bean products, coarse grains, nuts, fruits, mushrooms, and potatoes (β = 0.25, 95 % CI: 0.02-0.78 and β = 0.18, 95 % CI: 0.01-0.54).

CONCLUSIONS: Our findings highlight the complex interplay between dietary patterns, gut microbiota, and the risk of developing SD in young adults, underscoring the potential for dietary interventions and microbiome modulation in mental health promotion.},
}

Humans
Female
Male
*Gastrointestinal Microbiome
Young Adult
Adult
*Depression/microbiology
Cross-Sectional Studies
Adolescent
*Feeding Behavior
*Diet/methods
China
*Feces/microbiology
Incidence
Dietary Patterns
East Asian People

@article {pmid39423213,
year = {2024},
author = {Ma, J and Yang, X and He, J},
title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0305583},
doi = {10.1371/journal.pone.0305583},
pmid = {39423213},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; },
abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.},
}

Humans
*Gastrointestinal Microbiome
Aged
Aged, 80 and over
Adult
Middle Aged
Male
Aging
Young Adult
Microbial Interactions
Female
Bacteria/genetics/classification
Age Factors
Archaea/genetics

@article {pmid39422129,
year = {2024},
author = {Kanti Nath, B and Gupta, SD and Talukder, S and Tonu, NS and Raidal, SR and Forwood, JK and Sarker, S},
title = {Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.},
journal = {Veterinary medicine and science},
volume = {10},
number = {6},
pages = {e70083},
doi = {10.1002/vms3.70083},
pmid = {39422129},
issn = {2053-1095},
mesh = {Animals ; *Feces/virology/microbiology ; *Parakeets/virology ; Bird Diseases/virology/epidemiology/microbiology ; Australia ; Adenoviridae/isolation & purification/classification/genetics ; Parvoviridae/isolation & purification/genetics/classification ; Phylogeny ; Circovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/veterinary ; Victoria ; Circoviridae/isolation & purification/genetics/classification ; Virome ; Metagenomics ; },
abstract = {BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species.

OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing.

METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF).

RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis).

CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.},
}

Animals
*Feces/virology/microbiology
*Parakeets/virology
Bird Diseases/virology/epidemiology/microbiology
Australia
Adenoviridae/isolation & purification/classification/genetics
Parvoviridae/isolation & purification/genetics/classification
Phylogeny
Circovirus/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/veterinary
Victoria
Circoviridae/isolation & purification/genetics/classification
Virome
Metagenomics

@article {pmid39253815,
year = {2024},
author = {Wimmer, MI and Bartolomaeus, H and Anandakumar, H and Chen, CY and Vecera, V and Kedziora, S and Kamboj, S and Schumacher, F and Pals, S and Rauch, A and Meisel, J and Potapenko, O and Yarritu, A and Bartolomaeus, TUP and Samaan, M and Thiele, A and Stürzbecher, L and Geisberger, SY and Kleuser, B and Oefner, PJ and Haase, N and Löber, U and Gronwald, W and Forslund-Startceva, SK and Müller, DN and Wilck, N},
title = {Metformin modulates microbiota and improves blood pressure and cardiac remodeling in a rat model of hypertension.},
journal = {Acta physiologica (Oxford, England)},
volume = {240},
number = {11},
pages = {e14226},
doi = {10.1111/apha.14226},
pmid = {39253815},
issn = {1748-1716},
support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsches Zentrum für Herz-Kreislaufforschung/ ; },
mesh = {Animals ; *Metformin/pharmacology ; *Hypertension/drug therapy/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Blood Pressure/drug effects ; *Ventricular Remodeling/drug effects ; Rats ; *Rats, Transgenic ; Disease Models, Animal ; Hypoglycemic Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; },
abstract = {AIMS: Metformin has been attributed to cardiovascular protection even in the absence of diabetes. Recent observations suggest that metformin influences the gut microbiome. We aimed to investigate the influence of metformin on the gut microbiota and hypertensive target organ damage in hypertensive rats.

METHODS: Male double transgenic rats overexpressing the human renin and angiotensinogen genes (dTGR), a model of angiotensin II-dependent hypertension, were treated with metformin (300 mg/kg/day) or vehicle from 4 to 7 weeks of age. We assessed gut microbiome composition and function using shotgun metagenomic sequencing and measured blood pressure via radiotelemetry. Cardiac and renal organ damage and inflammation were evaluated by echocardiography, histology, and flow cytometry.

RESULTS: Metformin treatment increased the production of short-chain fatty acids (SCFA) acetate and propionate in feces without altering microbial composition and diversity. It significantly reduced systolic and diastolic blood pressure and improved cardiac function, as measured by end-diastolic volume, E/A, and stroke volume despite increased cardiac hypertrophy. Metformin reduced cardiac inflammation by lowering macrophage infiltration and shifting macrophage subpopulations towards a less inflammatory phenotype. The observed improvements in blood pressure, cardiac function, and inflammation correlated with fecal SCFA levels in dTGR. In vitro, acetate and propionate altered M1-like gene expression in macrophages, reinforcing anti-inflammatory effects. Metformin did not affect hypertensive renal damage or microvascular structure.

CONCLUSION: Metformin modulated the gut microbiome, increased SCFA production, and ameliorated blood pressure and cardiac remodeling in dTGR. Our findings confirm the protective effects of metformin in the absence of diabetes, highlighting SCFA as a potential mediators.},
}

Animals
*Metformin/pharmacology
*Hypertension/drug therapy/metabolism
Male
*Gastrointestinal Microbiome/drug effects
*Blood Pressure/drug effects
*Ventricular Remodeling/drug effects
Rats
*Rats, Transgenic
Disease Models, Animal
Hypoglycemic Agents/pharmacology
Fatty Acids, Volatile/metabolism

@article {pmid39420033,
year = {2024},
author = {Majzoub, ME and Paramsothy, S and Haifer, C and Parthasarathy, R and Borody, TJ and Leong, RW and Kamm, MA and Kaakoush, NO},
title = {The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8979},
pmid = {39420033},
issn = {2041-1723},
support = {988415//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; APP2011047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Investigator grant//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW Australia)/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/virology ; *Fecal Microbiota Transplantation ; *Bacteriophages/genetics/isolation & purification/physiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/virology ; Double-Blind Method ; Male ; Female ; Metagenomics/methods ; Adult ; Dysbiosis/microbiology/therapy ; Middle Aged ; Virome/genetics ; Remission Induction ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; },
abstract = {Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.},
}

Humans
*Colitis, Ulcerative/therapy/microbiology/virology
*Fecal Microbiota Transplantation
*Bacteriophages/genetics/isolation & purification/physiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology/virology
Double-Blind Method
Male
Female
Metagenomics/methods
Adult
Dysbiosis/microbiology/therapy
Middle Aged
Virome/genetics
Remission Induction
Anti-Bacterial Agents/therapeutic use
Biomarkers

@article {pmid39418241,
year = {2024},
author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z},
title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0310014},
doi = {10.1371/journal.pone.0310014},
pmid = {39418241},
issn = {1932-6203},
mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.},
}

Animals
*Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Metabolomics/methods
Rats
*Gastrointestinal Microbiome/drug effects
Male
*Rats, Sprague-Dawley
*Metagenomics/methods
Metabolome/drug effects
Feces/microbiology
Disease Models, Animal

@article {pmid39417540,
year = {2024},
author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S},
title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.94558},
pmid = {39417540},
issn = {2050-084X},
support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; },
mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; },
abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.},
}

*Rhizosphere
*Malus/microbiology/metabolism
*Microbiota
Plant Roots/microbiology/metabolism
Soil Microbiology
Bacteria/metabolism/genetics/classification
Crops, Agricultural/microbiology
Metabolomics/methods
Models, Biological

@article {pmid39298862,
year = {2024},
author = {Karadayı, S and Yılmaz, İ and Özbek, T and Karadayı, B},
title = {Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study.},
journal = {Journal of forensic and legal medicine},
volume = {107},
number = {},
pages = {102757},
doi = {10.1016/j.jflm.2024.102757},
pmid = {39298862},
issn = {1878-7487},
mesh = {Humans ; *Microbiota ; *Hand/microbiology ; *Touch ; RNA, Ribosomal, 16S ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/isolation & purification/genetics ; Female ; Adult ; },
abstract = {New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator.},
}

Humans
*Microbiota
*Hand/microbiology
*Touch
RNA, Ribosomal, 16S
Male
High-Throughput Nucleotide Sequencing
Bacteria/isolation & purification/genetics
Female
Adult

@article {pmid39179206,
year = {2024},
author = {Barone Lumaga, R and Tagliamonte, S and De Rosa, T and Valentino, V and Ercolini, D and Vitaglione, P},
title = {Consumption of a Sourdough-Leavened Croissant Enriched with a Blend of Fibers Influences Fasting Blood Glucose in a Randomized Controlled Trial in Healthy Subjects.},
journal = {The Journal of nutrition},
volume = {154},
number = {10},
pages = {2976-2987},
doi = {10.1016/j.tjnut.2024.08.015},
pmid = {39179206},
issn = {1541-6100},
mesh = {Humans ; *Dietary Fiber/administration & dosage/pharmacology ; Male ; Female ; *Blood Glucose/analysis ; Adult ; *Bread/analysis ; Gastrointestinal Microbiome ; Middle Aged ; Fasting ; Young Adult ; Healthy Volunteers ; Diet ; },
abstract = {BACKGROUND: An incorrect lifestyle, including diet, is responsible for the worldwide dramatic increase in obesity and type 2 diabetes. Increasing dietary fiber consumption may lead to health benefits, and reformulation of bakery products may be a strategy to globally improve the diet.

OBJECTIVES: This study aimed to assess the impact of a 2-wk breakfast consumption with a sourdough-leavened croissant containing a blend of dietary fiber from 10 sources (4.8 g/100 g, croissant enriched with dietary fibers [FIBCRO]), compared with a control croissant (dietary fibers 1.3 g/100 g, CONCRO) on daily energy intake, appetite, metabolic variables, and the gut microbiome.

METHODS: Thirty-two healthy participants were randomly allocated to 2 groups consuming FIBCRO or CONCRO. Participants self-recorded their diet and appetite through 7-d weighted food diaries and visual analog scales every day over the 2 wk. At baseline and after the intervention, fasting blood and urine samples, and fecal samples were collected beside blood pressure, anthropometry, and body composition. Serum glucose, lipids, C-reactive protein, and insulin according to the official methods and serum dipeptidyl peptidase-4 (DPPIV) activity by photometric method were measured. Polyphenols and urolithins in urines were analyzed by Liquid chromatography-tandem mass spectrometry (LC/MS/MS), whereas gut microbiome in feces by shotgun metagenomics.

RESULTS: FIBCRO consumption improved fasting blood glucose compared with CONCRO (mean changes from baseline -2.0 mg/dL in FIBCRO compared with +3.1 mg/dL in CONCRO, P = 0.022), also reducing serum DPPIV activity by 1.7 IU/L (P = 0.01) and increasing urinary excretion of urolithin A-sulfate by 6.9 ng/mg creatinine (P = 0.04) compared with baseline. No further changes in any of the monitored variables or in the gut microbiome were detected.

CONCLUSIONS: Results suggested that a 2-wk consumption of a sourdough croissant claimed as "source of dietary fiber" improved fasting glycemia compared with a conventional sourdough croissant in healthy subjects. The reduced serum DPPIV activity and increased bioavailability of urolithin likely contributed to determine that effect independently from gut microbiome changes. This trial was registered at clinicaltrials.gov as NCT04999280.},
}

Humans
*Dietary Fiber/administration & dosage/pharmacology
Male
Female
*Blood Glucose/analysis
Adult
*Bread/analysis
Gastrointestinal Microbiome
Middle Aged
Fasting
Young Adult
Healthy Volunteers
Diet

@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}

Humans
Hong Kong
*Microbiota
*Built Environment
*Metagenome
*Phylogeny
*Bacteria/classification/genetics/metabolism/isolation & purification
Skin/microbiology
Micrococcus luteus/genetics/metabolism
Genome, Bacterial

@article {pmid39414630,
year = {2024},
author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE},
title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {412},
pmid = {39414630},
issn = {1432-0991},
mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; },
abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.},
}

*Persea/microbiology
*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Soil/chemistry
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Plant Roots/microbiology
Colombia
Phylogeny

@article {pmid39409167,
year = {2024},
author = {Evseev, P and Gutnik, D and Evpak, A and Kasimova, A and Miroshnikov, K},
title = {Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910838},
pmid = {39409167},
issn = {1422-0067},
mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; *Genome, Viral ; Evolution, Molecular ; Phylogeny ; Archaea/virology/genetics ; Capsid Proteins/genetics ; },
abstract = {Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.},
}

*Bacteriophages/genetics/classification
*Computational Biology/methods
*Genome, Viral
Evolution, Molecular
Phylogeny
Archaea/virology/genetics
Capsid Proteins/genetics

@article {pmid39409144,
year = {2024},
author = {Donchev, D and Stoikov, I and Diukendjieva, A and Ivanov, IN},
title = {Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910817},
pmid = {39409144},
issn = {1422-0067},
support = {BG05M2OP001-1.002-0001-C04//European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020/ ; not applicable//Biocampus Sofia Association/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Milk/microbiology ; *Metagenomics/methods ; Animals ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Flocculation ; Benchmarking ; Microbiota/genetics ; Water Microbiology ; },
abstract = {Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.},
}

*RNA, Ribosomal, 16S/genetics
*Milk/microbiology
*Metagenomics/methods
Animals
*DNA, Bacterial/genetics/isolation & purification
*Bacteria/genetics/classification/isolation & purification
Flocculation
Benchmarking
Microbiota/genetics
Water Microbiology

@article {pmid39408280,
year = {2024},
author = {Nguyen, SM and Tran, TDC and Tran, TM and Wang, C and Wu, J and Cai, Q and Ye, F and Shu, XO},
title = {Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.},
journal = {Nutrients},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/nu16193313},
pmid = {39408280},
issn = {2072-6643},
support = {N/A//The Peanut Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Arachis ; Male ; Female ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Vietnam ; Diet ; Middle Aged ; },
abstract = {Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.},
}

Humans
*Gastrointestinal Microbiome
*Arachis
Male
Female
*Feces/microbiology
Adult
Bacteria/classification/genetics
Vietnam
Diet
Middle Aged

@article {pmid39407346,
year = {2024},
author = {Barcenilla, C and Cobo-Díaz, JF and Puente, A and Valentino, V and De Filippis, F and Ercolini, D and Carlino, N and Pinto, F and Segata, N and Prieto, M and López, M and Alvarez-Ordóñez, A},
title = {In-depth characterization of food and environmental microbiomes across different meat processing plants.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {199},
pmid = {39407346},
issn = {2049-2618},
support = {BOCYL-D-07072020-6//Junta de Castilla y León and the European Social Fund/ ; PRE2021-098910//Ministerio de Ciencia e Innovación, Spain/ ; },
mesh = {*Microbiota ; *Food Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Meat Products/microbiology ; *Food Handling ; Environmental Microbiology ; Meat/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals ; Phylogeny ; },
abstract = {BACKGROUND: Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS: The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS: Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.},
}

*Microbiota
*Food Microbiology
*Bacteria/classification/genetics/isolation & purification
*Meat Products/microbiology
*Food Handling
Environmental Microbiology
Meat/microbiology
RNA, Ribosomal, 16S/genetics
Animals
Phylogeny

@article {pmid39407345,
year = {2024},
author = {Salgado, JFM and Hervé, V and Vera, MAG and Tokuda, G and Brune, A},
title = {Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {201},
pmid = {39407345},
issn = {2049-2618},
mesh = {Animals ; *Isoptera/microbiology ; *Lignin/metabolism ; *Gastrointestinal Microbiome ; Phylogeny ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenome ; Polysaccharides/metabolism ; Genome, Bacterial ; Genomics ; Cellulose/metabolism ; },
abstract = {BACKGROUND: The microbial landscape within termite guts varies across termite families. The gut microbiota of lower termites (LT) is dominated by cellulolytic flagellates that sequester wood particles in their digestive vacuoles, whereas in the flagellate-free higher termites (HT), cellulolytic activity has been attributed to fiber-associated bacteria. However, little is known about the role of individual lineages in fiber digestion, particularly in LT.

RESULTS: We investigated the lignocellulolytic potential of 2223 metagenome-assembled genomes (MAGs) recovered from the gut metagenomes of 51 termite species. In the flagellate-dependent LT, cellulolytic enzymes are restricted to MAGs of Bacteroidota (Dysgonomonadaceae, Tannerellaceae, Bacteroidaceae, Azobacteroidaceae) and Spirochaetota (Breznakiellaceae) and reflect a specialization on cellodextrins, whereas their hemicellulolytic arsenal features activities on xylans and diverse heteropolymers. By contrast, the MAGs derived from flagellate-free HT possess a comprehensive arsenal of exo- and endoglucanases that resembles that of termite gut flagellates, underlining that Fibrobacterota and Spirochaetota occupy the cellulolytic niche that became vacant after the loss of the flagellates. Furthermore, we detected directly or indirectly oxygen-dependent enzymes that oxidize cellulose or modify lignin in MAGs of Pseudomonadota (Burkholderiales, Pseudomonadales) and Actinomycetota (Actinomycetales, Mycobacteriales), representing lineages located at the hindgut wall.

CONCLUSIONS: The results of this study refine our concept of symbiotic digestion of lignocellulose in termite guts, emphasizing the differential roles of specific bacterial lineages in both flagellate-dependent and flagellate-independent breakdown of cellulose and hemicelluloses, as well as a so far unappreciated role of oxygen in the depolymerization of plant fiber and lignin in the microoxic periphery during gut passage in HT. Video Abstract.},
}

Animals
*Isoptera/microbiology
*Lignin/metabolism
*Gastrointestinal Microbiome
Phylogeny
Bacteria/genetics/classification/isolation & purification/enzymology
Metagenome
Polysaccharides/metabolism
Genome, Bacterial
Genomics
Cellulose/metabolism

@article {pmid39406897,
year = {2024},
author = {Westmeijer, G and van Dam, F and Kietäväinen, R and González-Rosales, C and Bertilsson, S and Drake, H and Dopson, M},
title = {Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1332},
pmid = {39406897},
issn = {2399-3642},
support = {2018-04311//Vetenskapsrådet (Swedish Research Council)/ ; },
mesh = {*Groundwater/microbiology ; Sweden ; Microbiota/genetics ; Metagenome ; Phylogeny ; Deltaproteobacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.},
}

*Groundwater/microbiology
Sweden
Microbiota/genetics
Metagenome
Phylogeny
Deltaproteobacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid39404262,
year = {2024},
author = {Zhong, C and Yamanouchi, S and Li, Y and Chen, J and Wei, T and Wang, R and Zhou, K and Cheng, A and Hao, W and Liu, H and Konhauser, KO and Iwasaki, W and Qian, P-Y},
title = {Marine biofilms: cyanobacteria factories for the global oceans.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031724},
doi = {10.1128/msystems.00317-24},
pmid = {39404262},
issn = {2379-5077},
abstract = {UNLABELLED: Marine biofilms were newly revealed as a giant microbial diversity pool for global oceans. However, the cyanobacterial diversity in marine biofilms within the upper seawater column and its ecological and evolutionary implications remains undetermined. Here, we reconstructed a full picture of modern marine cyanobacteria habitats by re-analyzing 9.3 terabyte metagenomic data sets and 2,648 metagenome-assembled genomes (MAGs). The abundances of cyanobacteria lineages exclusively detected in marine biofilms were up to ninefold higher than those in seawater at similar sample size. Analyses revealed that cyanobacteria in marine biofilms are specialists with strong geographical and environmental constraints on their genome and functional adaption, which is in stark contrast to the generalistic features of seawater-derived cyanobacteria. Molecular dating suggests that the important diversifications in biofilm-forming cyanobacteria appear to coincide with the Great Oxidation Event (GOE), "boring billion" middle Proterozoic, and the Neoproterozoic Oxidation Event (NOE). These new insights suggest that marine biofilms are large and important cyanobacterial factories for the global oceans.

IMPORTANCE: Cyanobacteria, highly diverse microbial organisms, play a crucial role in Earth's oxygenation and biogeochemical cycling. However, their connection to these processes remains unclear, partly due to incomplete surveys of oceanic niches. Our study uncovered significant cyanobacterial diversity in marine biofilms, showing distinct niche differentiation compared to seawater counterparts. These patterns reflect three key stages of marine cyanobacterial diversification, coinciding with major geological events in the Earth's history.},
}

@article {pmid39399973,
year = {2024},
author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC},
title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39399973},
issn = {2047-217X},
support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; },
mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.},
}

*Isotope Labeling/methods
Reproducibility of Results
Microbiota/genetics
Metadata
Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome

@article {pmid39399231,
year = {2024},
author = {Scicchitano, D and Foresto, L and Laczny, CC and Cinti, N and Vitagliano, R and Halder, R and Morri, G and Turroni, S and D'Amico, F and Palladino, G and Fiori, J and Wilmes, P and Rampelli, S and Candela, M},
title = {A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children.},
journal = {One health (Amsterdam, Netherlands)},
volume = {19},
number = {},
pages = {100902},
pmid = {39399231},
issn = {2352-7714},
abstract = {To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.},
}

@article {pmid39394504,
year = {2024},
author = {Passarini, MRZ and Robayo, MIG and Ottoni, JR and Duarte, AWF and Rosa, LH},
title = {Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {11},
pages = {345},
pmid = {39394504},
issn = {1573-0972},
support = {Nº 205/2021//Program Institutional Triple Agenda EDITAL PRPPG/ ; },
mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Agriculture ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Biotechnology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Soil/chemistry ; Phylogeny ; Nitrogen/metabolism ; Microbiota ; },
abstract = {The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.},
}

*Soil Microbiology
Antarctic Regions
*Bacteria/classification/genetics/isolation & purification/metabolism
*Agriculture
*Fungi/classification/genetics/isolation & purification/metabolism
*Biotechnology
*Metagenomics
High-Throughput Nucleotide Sequencing
Soil/chemistry
Phylogeny
Nitrogen/metabolism
Microbiota

@article {pmid39390034,
year = {2024},
author = {Delanghe, L and De Boeck, I and Van Malderen, J and Allonsius, CN and Van Rillaer, T and Bron, PA and Claes, I and Hagendorens, M and Lebeer, S and Leysen, J},
title = {Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23659},
pmid = {39390034},
issn = {2045-2322},
support = {HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 852600/ERC_/European Research Council/International ; },
mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Microbiota ; *Skin/microbiology/pathology ; Female ; Adult ; Male ; Staphylococcus aureus/genetics/isolation & purification/pathogenicity ; Bacteria/classification/genetics ; Middle Aged ; Metagenomics/methods ; },
abstract = {Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.},
}

*Dermatitis, Atopic/microbiology
Humans
*Microbiota
*Skin/microbiology/pathology
Female
Adult
Male
Staphylococcus aureus/genetics/isolation & purification/pathogenicity
Bacteria/classification/genetics
Middle Aged
Metagenomics/methods

@article {pmid39390025,
year = {2024},
author = {Larsson, A and Ericson, U and Jönsson, D and Miari, M and Athanasiadis, P and Baldanzi, G and Brunkwall, L and Hellstrand, S and Klinge, B and Melander, O and Nilsson, PM and Fall, T and Maziarz, M and Orho-Melander, M},
title = {New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23723},
pmid = {39390025},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polypharmacy ; Male ; Female ; Middle Aged ; Sweden ; Aged ; Adult ; },
abstract = {Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Polypharmacy
Male
Female
Middle Aged
Sweden
Aged
Adult

@article {pmid39390011,
year = {2024},
author = {Kim, HS and Oh, SJ and Kim, BK and Kim, JE and Kim, BH and Park, YK and Yang, BG and Lee, JY and Bae, JW and Lee, CK},
title = {Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23701},
pmid = {39390011},
issn = {2045-2322},
support = {2017R1A5A2014768//National Research Foundation of Korea/ ; 2021R1C1C2008556//National Research Foundation of Korea/ ; HI23C0661//Korea Health Industry Development Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; Republic of Korea/epidemiology ; Adult ; Middle Aged ; *Biomarkers ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Colitis, Ulcerative/microbiology/diagnosis ; Metagenomics/methods ; Crohn Disease/microbiology/diagnosis ; Case-Control Studies ; Cross-Sectional Studies ; Young Adult ; Aged ; },
abstract = {Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Dysbiosis/diagnosis/microbiology
Female
Male
Republic of Korea/epidemiology
Adult
Middle Aged
*Biomarkers
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/diagnosis
Colitis, Ulcerative/microbiology/diagnosis
Metagenomics/methods
Crohn Disease/microbiology/diagnosis
Case-Control Studies
Cross-Sectional Studies
Young Adult
Aged

@article {pmid39389770,
year = {2024},
author = {Xu, Y and Yan, Y and Zhou, T and Lu, Y and Yang, X and Tang, K and Liu, F},
title = {Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c07428},
pmid = {39389770},
issn = {1520-5118},
abstract = {Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.},
}

@article {pmid39389057,
year = {2024},
author = {Hou, X and He, Y and Fang, P and Mei, SQ and Xu, Z and Wu, WC and Tian, JH and Zhang, S and Zeng, ZY and Gou, QY and Xin, GY and Le, SJ and Xia, YY and Zhou, YL and Hui, FM and Pan, YF and Eden, JS and Yang, ZH and Han, C and Shu, YL and Guo, D and Li, J and Holmes, EC and Li, ZR and Shi, M},
title = {Using artificial intelligence to document the hidden RNA virosphere.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.09.027},
pmid = {39389057},
issn = {1097-4172},
abstract = {Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.},
}

@article {pmid39389029,
year = {2024},
author = {Qian, J and Yeo, EN and Olm, MR},
title = {Hospitalization throws the preterm gut microbiome off-key.},
journal = {Cell host & microbe},
volume = {32},
number = {10},
pages = {1651-1653},
doi = {10.1016/j.chom.2024.09.009},
pmid = {39389029},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Feces/microbiology ; *Intensive Care Units, Neonatal ; *Metagenomics ; *Infant, Premature ; Hospitalization ; Infant ; },
abstract = {Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host & Microbe, Thänert et al.[1] characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Feces/microbiology
*Intensive Care Units, Neonatal
*Metagenomics
*Infant, Premature
Hospitalization
Infant

@article {pmid39384807,
year = {2024},
author = {Minot, SS and Li, N and Srinivasan, H and Ayers, JL and Yu, M and Koester, ST and Stangis, MM and Dominitz, JA and Halberg, RB and Grady, WM and Dey, N},
title = {Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23646},
pmid = {39384807},
issn = {2045-2322},
support = {K08 DK111941/DK/NIDDK NIH HHS/United States ; R50 CA233042/CA/NCI NIH HHS/United States ; U54 CA274374/CA/NCI NIH HHS/United States ; R50CA233042//U.S. Department of Health and Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; Mice ; *Bacteria/genetics/classification ; *Precancerous Conditions/microbiology ; Metagenomics/methods ; },
abstract = {The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23-40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of "known unknowns" of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.},
}

*Colorectal Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Animals
Humans
Mice
*Bacteria/genetics/classification
*Precancerous Conditions/microbiology
Metagenomics/methods

@article {pmid39380016,
year = {2024},
author = {Ju, Y and Zhang, Z and Liu, M and Lin, S and Sun, Q and Song, Z and Liang, W and Tong, X and Jie, Z and Lu, H and Cai, K and Chen, P and Jin, X and Zhang, W and Xu, X and Yang, H and Wang, J and Hou, Y and Xiao, L and Jia, H and Zhang, T and Guo, R},
title = {Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {257},
pmid = {39380016},
issn = {1474-760X},
mesh = {Humans ; Male ; Female ; *Metagenome ; *Microbiota ; Adult ; Nose/microbiology ; Sex Characteristics ; Young Adult ; Bacteria/genetics/classification ; Sex Factors ; Metagenomics/methods ; },
abstract = {BACKGROUND: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.

RESULTS: Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.

CONCLUSIONS: In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.},
}

Humans
Male
Female
*Metagenome
*Microbiota
Adult
Nose/microbiology
Sex Characteristics
Young Adult
Bacteria/genetics/classification
Sex Factors
Metagenomics/methods

@article {pmid39379175,
year = {2024},
author = {Zheng, D and Wilén, BM and Öberg, O and Wik, T and Modin, O},
title = {"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".},
journal = {Environmental microbiology},
volume = {26},
number = {10},
pages = {e16696},
doi = {10.1111/1462-2920.16696},
pmid = {39379175},
issn = {1462-2920},
support = {2020-02639//Svenska Forskningsrådet Formas/ ; },
mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Aquaculture ; *Naphthols/metabolism ; *Camphanes/metabolism ; Phylogeny ; Archaea/genetics/metabolism/classification ; Microbiota ; Metagenome ; },
abstract = {Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.},
}

*Metagenomics
*Bacteria/genetics/classification/metabolism
*Aquaculture
*Naphthols/metabolism
*Camphanes/metabolism
Phylogeny
Archaea/genetics/metabolism/classification
Microbiota
Metagenome

@article {pmid39378072,
year = {2024},
author = {Koohi-Moghadam, M and Watt, RM and Leung, WK},
title = {Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001898},
pmid = {39378072},
issn = {1473-5644},
mesh = {Humans ; *Periodontitis/microbiology ; *Multigene Family ; *Mouth/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pilot Projects ; Metagenomics/methods ; Saliva/microbiology ; Adult ; Male ; Biosynthetic Pathways/genetics ; Female ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Metagenome ; },
abstract = {Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.},
}

Humans
*Periodontitis/microbiology
*Multigene Family
*Mouth/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Pilot Projects
Metagenomics/methods
Saliva/microbiology
Adult
Male
Biosynthetic Pathways/genetics
Female
Middle Aged
High-Throughput Nucleotide Sequencing
Metagenome

@article {pmid39375774,
year = {2024},
author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K},
title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {195},
pmid = {39375774},
issn = {2049-2618},
mesh = {*Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; *Metagenomics/methods ; Humans ; *Metagenome ; *Genome, Viral/genetics ; Microbiota/genetics ; Soil Microbiology ; Fresh Water/virology/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.},
}

*Virome/genetics
*Viruses/genetics/classification/isolation & purification
*Metagenomics/methods
Humans
*Metagenome
*Genome, Viral/genetics
Microbiota/genetics
Soil Microbiology
Fresh Water/virology/microbiology
Gastrointestinal Microbiome/genetics

@article {pmid39375348,
year = {2024},
author = {Kang, X and Zhang, W and Li, Y and Luo, X and Schönhuth, A},
title = {HyLight: Strain aware assembly of low coverage metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8665},
pmid = {39375348},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Software ; },
abstract = {Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.},
}

*Metagenome/genetics
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Microbiota/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification
Genome, Bacterial
Software

@article {pmid39375018,
year = {2024},
author = {Yang, Q and Zhong, Y and Feng, SW and Wen, P and Wang, H and Wu, J and Yang, S and Liang, JL and Li, D and Yang, Q and Tam, NFY and Peng, P},
title = {Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39375018},
issn = {1751-7370},
support = {42 077 285//National Natural Science Foundation of China/ ; 2024A04J6534//Science and Technology Projects of Guangzhou/ ; ZDYF2023SHFZ171//Key Research and Development Program of Hainan Province/ ; 2023B1212060049//Guangdong Foundation for Program of Science and Technology Research/ ; 2023B0303000007//Guangdong Major Project of Basic and Applied Basic Research/ ; SKLOG2024-01//State Key Laboratory of Organic Geochemistry/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ammonia/metabolism ; *Nitrification ; Microbiota ; Bacteria/classification/genetics/metabolism/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Archaea/metabolism/genetics/classification/isolation & purification ; Metagenome ; },
abstract = {Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.},
}

*RNA, Ribosomal, 16S/genetics
*Seawater/microbiology
*Ammonia/metabolism
*Nitrification
Microbiota
Bacteria/classification/genetics/metabolism/isolation & purification
Oxidation-Reduction
Phylogeny
Archaea/metabolism/genetics/classification/isolation & purification
Metagenome

@article {pmid39369255,
year = {2024},
author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Hinzke, T and Maaß, S and Trautwein-Schult, A and Starke, J and Moore, CJ and Esser, SP and Plewka, J and Hesse, T and Schmidt, TC and Schreiber, U and Bor, B and Becher, D and Probst, AJ},
title = {Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {194},
pmid = {39369255},
issn = {2049-2618},
support = {CRC 1439/1 426547801//German Research Foundation (DFG)/ ; CRC 1439/1 426547801//German Research Foundation (DFG)/ ; },
mesh = {*Groundwater/microbiology ; Carbon Dioxide/metabolism ; Metagenomics ; Bacteria/genetics/classification/isolation & purification/metabolism ; Germany ; Genome, Bacterial ; Phylogeny ; Microbiota/genetics ; Proteogenomics ; Adaptation, Physiological ; Proteomics ; },
abstract = {BACKGROUND: Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS: We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS: We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.},
}

*Groundwater/microbiology
Carbon Dioxide/metabolism
Metagenomics
Bacteria/genetics/classification/isolation & purification/metabolism
Germany
Genome, Bacterial
Phylogeny
Microbiota/genetics
Proteogenomics
Adaptation, Physiological
Proteomics

@article {pmid39367431,
year = {2024},
author = {Gaber, M and Wilson, AS and Millen, AE and Hovey, KM and LaMonte, MJ and Wactawski-Wende, J and Ochs-Balcom, HM and Cook, KL},
title = {Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {192},
pmid = {39367431},
issn = {2049-2618},
support = {W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; },
mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; *Endotoxemia/immunology/microbiology ; Humans ; *Postmenopause ; Animals ; Aged ; Mice ; *Lipopolysaccharides ; Intra-Abdominal Fat/metabolism/immunology ; Inflammation ; Aged, 80 and over ; Mice, Inbred C57BL ; Adiposity ; Bacteria/classification/isolation & purification/metabolism/genetics ; Acute-Phase Proteins/metabolism ; Feces/microbiology ; Obesity, Abdominal/microbiology/immunology ; Absorptiometry, Photon ; Carrier Proteins ; Membrane Glycoproteins ; },
abstract = {BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS: Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm[2]) and n = 25 with high VAT area (177.5 ± 31.3 cm[2]). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS: Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS: Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.},
}

Female
*Gastrointestinal Microbiome/drug effects
*Endotoxemia/immunology/microbiology
Humans
*Postmenopause
Animals
Aged
Mice
*Lipopolysaccharides
Intra-Abdominal Fat/metabolism/immunology
Inflammation
Aged, 80 and over
Mice, Inbred C57BL
Adiposity
Bacteria/classification/isolation & purification/metabolism/genetics
Acute-Phase Proteins/metabolism
Feces/microbiology
Obesity, Abdominal/microbiology/immunology
Absorptiometry, Photon
Carrier Proteins
Membrane Glycoproteins

@article {pmid39367018,
year = {2024},
author = {Baldi, A and Braat, S and Hasan, MI and Bennett, C and Barrios, M and Jones, N and Abdul Azeez, I and Wilcox, S and Roy, PK and Bhuiyan, MSA and Ataide, R and Clucas, D and Larson, LM and Hamadani, J and Zimmermann, M and Bowden, R and Jex, A and Biggs, BA and Pasricha, SR},
title = {Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8640},
pmid = {39367018},
issn = {2041-1723},
support = {GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2009047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Bangladesh ; *Dietary Supplements ; *Micronutrients/administration & dosage ; Female ; *Iron/metabolism/administration & dosage ; Male ; *RNA, Ribosomal, 16S/genetics ; *Powders ; Diarrhea/microbiology ; Feces/microbiology ; Anemia, Iron-Deficiency/microbiology ; },
abstract = {Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. Small studies in Africa indicate iron may reprofile the gut microbiome towards pathogenic species. We seek to evaluate the safety of iron and MNPs based on their effects on diversity, composition, and function of the gut microbiome in children in rural Bangladesh as part of a large placebo-controlled randomized controlled trial of iron or MNPs given for 3 months (ACTRN12617000660381). In 923 infants, we evaluate the microbiome before, immediately following, and nine months after interventions, using 16S rRNA gene sequencing and shotgun metagenomics in a subset. We identify no increase in diarrhea with either treatment. In our primary analysis, neither iron nor MNPs alter gut microbiome diversity or composition. However, when not adjusting for multiple comparisons, compared to placebo, children receiving iron and MNPs exhibit reductions in commensal species (e.g., Bifidobacterium, Lactobacillus) and increases in potential pathogens, including Clostridium. These increases are most evident in children with baseline iron repletion and are further supported by trend-based statistical analyses.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Infant
Bangladesh
*Dietary Supplements
*Micronutrients/administration & dosage
Female
*Iron/metabolism/administration & dosage
Male
*RNA, Ribosomal, 16S/genetics
*Powders
Diarrhea/microbiology
Feces/microbiology
Anemia, Iron-Deficiency/microbiology

@article {pmid39361891,
year = {2024},
author = {Ramos-Barbero, MD and Gómez-Gómez, C and Vique, G and Sala-Comorera, L and Rodríguez-Rubio, L and Muniesa, M},
title = {Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39361891},
issn = {1751-7370},
mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral ; *Phylogeny ; *Virome/genetics ; *Chickens/virology ; Feces/virology ; Host Specificity ; },
abstract = {The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.},
}

Humans
*Bacteriophages/genetics/classification/isolation & purification
Animals
*Genome, Viral
*Phylogeny
*Virome/genetics
*Chickens/virology
Feces/virology
Host Specificity

@article {pmid39358810,
year = {2024},
author = {Meng, L and Jin, H and Yulug, B and Altay, O and Li, X and Hanoglu, L and Cankaya, S and Coskun, E and Idil, E and Nogaylar, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Borén, J and Uhlén, M and Mardinoglu, A},
title = {Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.},
journal = {Alzheimer's research & therapy},
volume = {16},
number = {1},
pages = {213},
pmid = {39358810},
issn = {1758-9193},
mesh = {Humans ; *Alzheimer Disease/genetics/microbiology/metabolism/blood ; *Proteomics ; Female ; Male ; Aged ; *Metabolomics/methods ; *Gastrointestinal Microbiome ; Severity of Illness Index ; Artificial Intelligence ; Aged, 80 and over ; Biomarkers/blood ; Metagenomics/methods ; Multiomics ; },
abstract = {Alzheimer's disease (AD) is a debilitating neurodegenerative disorder with a global impact, yet its pathogenesis remains poorly understood. While age, metabolic abnormalities, and accumulation of neurotoxic substances are potential risk factors for AD, their effects are confounded by other factors. To address this challenge, we first utilized multi-omics data from 87 well phenotyped AD patients and generated plasma proteomics and metabolomics data, as well as gut and saliva metagenomics data to investigate the molecular-level alterations accounting the host-microbiome interactions. Second, we analyzed individual omics data and identified the key parameters involved in the severity of the dementia in AD patients. Next, we employed Artificial Intelligence (AI) based models to predict AD severity based on the significantly altered features identified in each omics analysis. Based on our integrative analysis, we found the clinical relevance of plasma proteins, including SKAP1 and NEFL, plasma metabolites including homovanillate and glutamate, and Paraprevotella clara in gut microbiome in predicting the AD severity. Finally, we validated the predictive power of our AI based models by generating additional multi-omics data from the same group of AD patients by following up for 3 months. Hence, we observed that these results may have important implications for the development of potential diagnostic and therapeutic approaches for AD patients.},
}

Humans
*Alzheimer Disease/genetics/microbiology/metabolism/blood
*Proteomics
Female
Male
Aged
*Metabolomics/methods
*Gastrointestinal Microbiome
Severity of Illness Index
Artificial Intelligence
Aged, 80 and over
Biomarkers/blood
Metagenomics/methods
Multiomics

@article {pmid39358791,
year = {2024},
author = {Wirajana, IN and Ariantari, NP and Shyu, DJH and Vaghamshi, N and Antaliya, K and Dudhagara, P},
title = {Prokaryotic communities profiling of Indonesian hot springs using long-read Oxford Nanopore sequencing.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {286},
pmid = {39358791},
issn = {1756-0500},
support = {B/530-4/UN14.4A/PT.01.03/2023//Udayana University International Senior Fellowship (UNISERF) grant for year 2023 (Grant Number: B/530-4/UN14.4A/PT.01.03/2023), Udayana University, Bali, Indonesia/ ; },
mesh = {*Hot Springs/microbiology ; Indonesia ; *RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing/methods ; Microbiota/genetics ; Bacteria/genetics/isolation & purification/classification ; Metagenome/genetics ; Metagenomics/methods ; Water Microbiology ; Phylogeny ; DNA, Bacterial/genetics/analysis ; Sequence Analysis, DNA/methods ; },
abstract = {OBJECTIVES: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile.

DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.},
}

*Hot Springs/microbiology
Indonesia
*RNA, Ribosomal, 16S/genetics
*Nanopore Sequencing/methods
Microbiota/genetics
Bacteria/genetics/isolation & purification/classification
Metagenome/genetics
Metagenomics/methods
Water Microbiology
Phylogeny
DNA, Bacterial/genetics/analysis
Sequence Analysis, DNA/methods

@article {pmid39358771,
year = {2024},
author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M},
title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {188},
pmid = {39358771},
issn = {2049-2618},
mesh = {Humans ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Mouth/microbiology ; *Genome, Bacterial ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Phylogeny ; },
abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.},
}

Humans
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
*Mouth/microbiology
*Genome, Bacterial
Interspersed Repetitive Sequences/genetics
Microbiota/genetics
Drug Resistance, Bacterial/genetics
Metagenomics/methods
Phylogeny

@article {pmid39356745,
year = {2024},
author = {Hartman, SJ and Hibberd, MC and Mostafa, I and Naila, NN and Islam, MM and Zaman, MU and Huq, S and Mahfuz, M and Islam, MT and Mukherji, K and Moghaddam, VA and Chen, RY and Province, MA and Webber, DM and Henrissat, S and Henrissat, B and Terrapon, N and Rodionov, DA and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI},
title = {A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.},
journal = {Science translational medicine},
volume = {16},
number = {767},
pages = {eadn2366},
doi = {10.1126/scitranslmed.adn2366},
pmid = {39356745},
issn = {1946-6242},
mesh = {Humans ; *Severe Acute Malnutrition/diet therapy/therapy ; Infant ; Microbiota ; Male ; Female ; Bangladesh ; Gastrointestinal Microbiome ; },
abstract = {Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10[-3]), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10[-6]). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.},
}

Humans
*Severe Acute Malnutrition/diet therapy/therapy
Infant
Microbiota
Male
Female
Bangladesh
Gastrointestinal Microbiome

@article {pmid39354019,
year = {2024},
author = {Oaikhena, AO and Coker, ME and Cyril-Okoh, D and Wicaksono, WA and Olimi, E and Berg, G and Okeke, IN},
title = {The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22806},
pmid = {39354019},
issn = {2045-2322},
support = {INV-036234/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {*Euphorbia ; *Ficus/microbiology ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; *Fungi/genetics/classification/isolation & purification ; Nigeria ; Phylogeny ; },
abstract = {The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10[8] per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.},
}

*Euphorbia
*Ficus/microbiology
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Bacteria/genetics/classification/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Plant Leaves/microbiology
*Fungi/genetics/classification/isolation & purification
Nigeria
Phylogeny

@article {pmid39354003,
year = {2024},
author = {Li, Y and Liu, H and Xiao, Y and Jing, H},
title = {Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1067},
pmid = {39354003},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Archaea/genetics ; *Phylogeny ; *Bacteria/genetics/classification ; Genome, Microbial ; Microbiota ; Genome, Archaeal ; },
abstract = {Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.},
}

*Geologic Sediments/microbiology
*Metagenome
*Archaea/genetics
*Phylogeny
*Bacteria/genetics/classification
Genome, Microbial
Microbiota
Genome, Archaeal

@article {pmid39351905,
year = {2024},
author = {Feng, M and Robinson, S and Qi, W and Edwards, A and Stierli, B and van der Heijden, M and Frey, B and Varliero, G},
title = {Microbial genetic potential differs among cryospheric habitats of the Damma glacier.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
pmid = {39351905},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology ; *Ecosystem ; Soil Microbiology ; Nitrogen Fixation/genetics ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Nitrogen Cycle/genetics ; },
abstract = {Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.},
}

*Ice Cover/microbiology
*Ecosystem
Soil Microbiology
Nitrogen Fixation/genetics
Microbiota/genetics
Metagenomics
Geologic Sediments/microbiology
Bacteria/genetics/classification/isolation & purification
Metagenome
Nitrogen Cycle/genetics

@article {pmid39351368,
year = {2024},
author = {Tolstoganov, I and Chen, Z and Pevzner, P and Korobeynikov, A},
title = {SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18050},
pmid = {39351368},
issn = {2167-8359},
mesh = {*Diploidy ; Animals ; Humans ; Genome, Human/genetics ; Sheep/genetics ; Software ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; },
abstract = {BACKGROUND: Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.

RESULTS: We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.

CONCLUSION: We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.},
}

*Diploidy
Animals
Humans
Genome, Human/genetics
Sheep/genetics
Software
Sequence Analysis, DNA/methods
Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
Genome/genetics

@article {pmid39349486,
year = {2024},
author = {Sun, W and Zhang, Y and Guo, R and Sha, S and Chen, C and Ullah, H and Zhang, Y and Ma, J and You, W and Meng, J and Lv, Q and Cheng, L and Fan, S and Li, R and Mu, X and Li, S and Yan, Q},
title = {A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {96},
pmid = {39349486},
issn = {2055-5008},
support = {5050071720001//Beijing University of Chinese Medicine (BUCM)/ ; 2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81503455//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; China ; Biodiversity ; },
abstract = {The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.},
}

Humans
*Gastrointestinal Microbiome
*Feces/microbiology
Case-Control Studies
*Bacteria/classification/genetics/isolation & purification
Metagenome
Metagenomics/methods
China
Biodiversity

@article {pmid39347539,
year = {2024},
author = {Yuan, Y and Hu, H and Sun, Z and Wang, W and Wang, Z and Zheng, M and Xing, Y and Zhang, W and Wang, M and Lu, X and Li, Y and Liang, C and Lin, Z and Xie, C and Li, J and Mao, T},
title = {Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice.},
journal = {Drug design, development and therapy},
volume = {18},
number = {},
pages = {4273-4289},
pmid = {39347539},
issn = {1177-8881},
mesh = {Animals ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Inflammatory Bowel Diseases/drug therapy ; *Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Network Pharmacology ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; RNA-Seq ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.

PURPOSE: We aimed to probe the mechanism of QCWZD for the treatment of IBD.

METHODS: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.

RESULTS: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3[+]CD4[+]IL-17[+] (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-κB, TNF-α and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.

CONCLUSION: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD.},
}

Animals
Mice
*Drugs, Chinese Herbal/pharmacology/chemistry
*Inflammatory Bowel Diseases/drug therapy
*Metagenomics
*Gastrointestinal Microbiome/drug effects
*Network Pharmacology
*Dextran Sulfate
*Mice, Inbred C57BL
Disease Models, Animal
Male
RNA-Seq

@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}

*Nanopore Sequencing/methods
Metagenomics/methods
Plant Diseases/microbiology
Bacteria/genetics/isolation & purification/classification
Sequence Analysis, DNA/methods
Fungi/genetics/isolation & purification/classification
Plants/microbiology
Computational Biology/methods

@article {pmid39343535,
year = {2024},
author = {Masuda, N and Kato, S and Ohkuma, M and Endo, K},
title = {Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.},
journal = {Microbes and environments},
volume = {39},
number = {3},
pages = {},
pmid = {39343535},
issn = {1347-4405},
mesh = {*Sulfides/metabolism ; *Gammaproteobacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Seawater/microbiology ; *Metagenome ; Geologic Sediments/microbiology/chemistry ; Phylogeny ; Ecosystem ; Pacific Ocean ; Oxidation-Reduction ; Microbiota/genetics ; Carbon Cycle ; },
abstract = {Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.},
}

*Sulfides/metabolism
*Gammaproteobacteria/genetics/classification/isolation & purification
*Metagenomics
*Seawater/microbiology
*Metagenome
Geologic Sediments/microbiology/chemistry
Phylogeny
Ecosystem
Pacific Ocean
Oxidation-Reduction
Microbiota/genetics
Carbon Cycle

@article {pmid39342753,
year = {2024},
author = {Zou, S and Hu, R and Liang, S and Lu, T and Kang, D and Li, D},
title = {Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {285},
number = {},
pages = {117117},
doi = {10.1016/j.ecoenv.2024.117117},
pmid = {39342753},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Humans ; *Animals, Wild/microbiology ; Risk Assessment ; Colobinae/microbiology/genetics ; Metagenomics ; Metagenome ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology/toxicity ; },
abstract = {Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Ecosystem
*Drug Resistance, Microbial/genetics
Humans
*Animals, Wild/microbiology
Risk Assessment
Colobinae/microbiology/genetics
Metagenomics
Metagenome
Environmental Monitoring
Anti-Bacterial Agents/pharmacology/toxicity

@article {pmid39342284,
year = {2024},
author = {Seitz, VA and McGivern, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC},
title = {Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {183},
pmid = {39342284},
issn = {2049-2618},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; 507580//Facilities Integrating Collaborations for User Science/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; P30CA046934//Cancer Center Support Grant/ ; },
mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Crops, Agricultural/microbiology ; *Microbiota ; *Rhizosphere ; *Soil/chemistry ; Bacteria/classification/metabolism/isolation & purification ; Agriculture ; Plant Growth Regulators/metabolism ; Plant Exudates/metabolism ; Sorghum/metabolism/microbiology ; },
abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production. Video Abstract.},
}

*Soil Microbiology
*Plant Roots/microbiology
*Crops, Agricultural/microbiology
*Microbiota
*Rhizosphere
*Soil/chemistry
Bacteria/classification/metabolism/isolation & purification
Agriculture
Plant Growth Regulators/metabolism
Plant Exudates/metabolism
Sorghum/metabolism/microbiology

@article {pmid39342129,
year = {2024},
author = {García-Estrada, DA and Selem-Mojica, N and Martínez-Hernández, A and Lara-Reyna, J and Dávila-Ramos, S and Verdel-Aranda, K},
title = {Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {376},
pmid = {39342129},
issn = {1471-2180},
support = {No. 320237//Consejo Nacional de Humanidades, Ciencias y Tecnologías, México/ ; },
mesh = {*Wetlands ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodiversity ; Metagenomics ; Phylogeny ; DNA, Bacterial/genetics ; Soil Microbiology ; },
abstract = {BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.},
}

*Wetlands
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Biodiversity
Metagenomics
Phylogeny
DNA, Bacterial/genetics
Soil Microbiology

@article {pmid39342083,
year = {2024},
author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J},
title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {377},
pmid = {39342083},
issn = {1471-2180},
support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; },
mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; },
abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.},
}

Humans
*Kidney Failure, Chronic/therapy/metabolism/microbiology
*Gastrointestinal Microbiome
*Peritoneal Dialysis
*Sesquiterpenes/metabolism
Male
Female
*Feces/microbiology
Middle Aged
*Triterpenes/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Biosynthetic Pathways
Adult
Metagenomics
Aged

@article {pmid39341403,
year = {2024},
author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F},
title = {Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.},
journal = {The Journal of infection},
volume = {89},
number = {5},
pages = {106284},
doi = {10.1016/j.jinf.2024.106284},
pmid = {39341403},
issn = {1532-2742},
abstract = {OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.

METHODS: We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.

RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.

CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.},
}

@article {pmid39341154,
year = {2024},
author = {Gough, EK and Edens, TJ and Carr, L and Robertson, RC and Mutasa, K and Ntozini, R and Chasekwa, B and Geum, HM and Baharmand, I and Gill, SK and Mutasa, B and Mbuya, MNN and Majo, FD and Tavengwa, N and Francis, F and Tome, J and Evans, C and Kosek, M and Prendergast, AJ and Manges, AR and , },
title = {Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.},
journal = {EBioMedicine},
volume = {108},
number = {},
pages = {105362},
pmid = {39341154},
issn = {2352-3964},
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Growth Disorders/prevention & control/microbiology ; Female ; Male ; Zimbabwe ; Fucosyltransferases/genetics ; Feces/microbiology ; Bifidobacterium ; Dietary Supplements ; Nutrients ; },
abstract = {BACKGROUND: Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.

METHODS: We investigated whether mother-infant FUT status (n = 792) and infant gut microbiome composition (n = 354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.

FINDINGS: We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences -32.6% [95% CI: -55.3%, -9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences -68.1% [95% CI: -99.0%, -28.5%); and (iii) greater relative abundance of B. longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B. longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.

INTERPRETATION: These findings indicate that a persistently "younger" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.

FUNDING: Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.},
}

Humans
Infant
*Gastrointestinal Microbiome
*Growth Disorders/prevention & control/microbiology
Female
Male
Zimbabwe
Fucosyltransferases/genetics
Feces/microbiology
Bifidobacterium
Dietary Supplements
Nutrients

@article {pmid39340684,
year = {2024},
author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A},
title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {120},
pmid = {39340684},
issn = {1432-184X},
mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention & control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; },
abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.},
}

Animals
*Solanum lycopersicum/microbiology/parasitology
*Soil Microbiology
*Rhizosphere
*Bacillus/genetics/physiology
*Plant Roots/microbiology/parasitology
*Pest Control, Biological
Plant Diseases/parasitology/prevention & control/microbiology
Trichoderma/physiology/genetics
Tylenchoidea/physiology
Microbiota
Antinematodal Agents/pharmacology
Biological Control Agents/pharmacology
Bacteria/genetics/classification

@article {pmid39340212,
year = {2024},
author = {Avellaneda-Franco, L and Xie, L and Nakai, M and Barr, JJ and Marques, FZ},
title = {Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2407047},
doi = {10.1080/19490976.2024.2407047},
pmid = {39340212},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; Mice ; Male ; *Hypertension/virology ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; Angiotensin II/metabolism ; Genome, Viral ; },
abstract = {The gut microbiome is an emerging factor in preventing hypertension, yet the influence of gut bacteriophages, viruses infecting bacteria, on this condition remains unclear. Bacteriophage-bacteria interactions, which impact the gut microbiome, are influenced differentially by temperate and virulent bacteriophages. However, the standard technique for studying viral populations, viral-like particles (VLPs)-metagenomes, often overlook prophages, the intracellular stage of temperate bacteriophages, creating a knowledge gap. To address this, we investigated alterations in extracellular and intracellular bacteriophages, alongside bacterial populations, in the angiotensin II-hypertension model. We sequenced VLPs and bulk DNA from cecal-colonic samples collected from male C57BL/6J mice implanted with minipumps containing saline or angiotensin II. We assembled 106 bacterial and 816 viral genomes and found that gut viral and bacterial populations remained stable between hypertensive and normotensive mice. A higher number of temperate viruses were observed across all treatments. Although temperate viruses outnumbered virulent viruses, sequencing of both VLPs and bulk revealed that virions from virulent viruses were more abundant in the murine gut. We then evaluated the impact of low- and high-fiber intake on gut microbiome composition in the angiotensin II model. Fiber intake significantly influenced the gut microbiome composition and hypertension development. Mice receiving high-fiber had lower blood pressure, a higher bacterial-encoded carbohydrate-associated enzyme, and a higher total relative abundance of temperate viruses than those receiving low-fiber. Our findings suggest that phages are not associated with hypertension development in the angiotensin II model. However, they support a complex diet-bacteria/phage interaction that may be involved in blood pressure regulation.},
}

Animals
*Gastrointestinal Microbiome
*Dietary Fiber/administration & dosage
Mice
Male
*Hypertension/virology
*Mice, Inbred C57BL
*Bacteria/classification/genetics/isolation & purification
*Bacteriophages/physiology/genetics
*Disease Models, Animal
Angiotensin II/metabolism
Genome, Viral

@article {pmid39338979,
year = {2024},
author = {Opitz-Ríos, C and Burgos-Pacheco, A and Paredes-Cárcamo, F and Campanini-Salinas, J and Medina, DA},
title = {Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39338979},
issn = {2076-0817},
support = {11230295//Agencia Nacional de Investigación y Desarrollo/ ; VRID_FAPPE21-07//Universidad San Sebastián/ ; VRID_INTER23/02//Universidad San Sebastián/ ; VRID_DocI22/06//Universidad San Sebastián/ ; },
abstract = {Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.},
}

@article {pmid39338129,
year = {2024},
author = {Mayer, MH and Woldemariam, S and Gisinger, C and Dorner, TE},
title = {Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {9},
pages = {},
pmid = {39338129},
issn = {1660-4601},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sarcopenia/microbiology/physiopathology ; *Muscle Strength ; Aged ; *Muscle, Skeletal/microbiology/physiology ; Middle Aged ; Aged, 80 and over ; },
abstract = {Sarcopenia, characterized by reduced muscle mass, strength, or performance, is a common condition in older adults. The association between the gut microbiome and sarcopenia remains poorly understood. This systematic review aims to evaluate the relationship between muscle parameters and the intestinal microbiome. A systematic search was conducted in PubMed, EMBASE, Cochrane Library, and Google Scholar for studies published between 2002 and 2022 involving participants aged 50+. Studies were included if they assessed sarcopenia using at least one measure of muscle mass (skeletal muscle mass, bioelectrical impedance analysis, MRI), muscle strength, or muscle performance (SARC-F questionnaire, Timed-Up-and-Go Test, Chair Stand Test, grip strength, gait speed, Short Physical Performance Battery, 400 m Walk Test). The microbiome was measured using at least RNA/DNA sequencing or shotgun metagenomic sequencing. Twelve studies were analyzed. Findings revealed that a higher abundance of bacterial species such as Desulfovibrio piger, and Clostridium symbiosum and reduced diversity of butyrate-producing bacteria was associated with sarcopenia severity, as indicated by decreased grip strength, muscle mass, or physical performance. The gut microbiome plays a significant role in age-related muscle loss. Probiotics, prebiotics, and bacterial products could be potential interventions to improve muscle health in older adults.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sarcopenia/microbiology/physiopathology
*Muscle Strength
Aged
*Muscle, Skeletal/microbiology/physiology
Middle Aged
Aged, 80 and over

@article {pmid39334245,
year = {2024},
author = {Van Herzele, C and Coppens, S and Vereecke, N and Theuns, S and de Graaf, DC and Nauwynck, H},
title = {New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {118},
pmid = {39334245},
issn = {1297-9716},
support = {1SB3123N//Fonds Wetenschappelijk Onderzoek/ ; Baekeland mandate HBC.2020.2889//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Seasons ; *Hemolymph/virology/microbiology ; Nanopore Sequencing/methods/veterinary ; Bacteria/genetics/isolation & purification/classification ; Virome ; },
abstract = {Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.},
}

Animals
Bees/virology/microbiology
*Seasons
*Hemolymph/virology/microbiology
Nanopore Sequencing/methods/veterinary
Bacteria/genetics/isolation & purification/classification
Virome

@article {pmid39333778,
year = {2024},
author = {Msango, K and Gouda, MNR and Ramakrishnan, B and Kumar, A and Subramanian, S},
title = {Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22400},
pmid = {39333778},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/microbiology ; *Cellulose/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Symbiosis ; },
abstract = {This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.},
}

Animals
*Coleoptera/microbiology
*Cellulose/metabolism
*Gastrointestinal Microbiome
*Bacteria/genetics/metabolism/classification/isolation & purification
Larva/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
Symbiosis

@article {pmid39333734,
year = {2024},
author = {Ishak, S and Rondeau-Leclaire, J and Faticov, M and Roy, S and Laforest-Lapointe, I},
title = {Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22168},
pmid = {39333734},
issn = {2045-2322},
mesh = {*Bryophyta/microbiology ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; Taiga ; Metagenomics/methods ; Microbiota ; Quebec ; Nitrogen Fixation ; Photosynthesis ; },
abstract = {Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.},
}

*Bryophyta/microbiology
*Bacteria/genetics/metabolism/classification
*Metagenome
Taiga
Metagenomics/methods
Microbiota
Quebec
Nitrogen Fixation
Photosynthesis

@article {pmid39333577,
year = {2024},
author = {Zhao, B and Zi, M and Zhang, X and Wang, Y},
title = {Microbial communities and metagenomes in methane-rich deep coastal sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1043},
pmid = {39333577},
issn = {2052-4463},
support = {U22B2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; *Archaea/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Coastal sediments are rich in embedded recalcitrant organic carbons that are biotransformed into methane. In this study, gas composition (carbon dioxide, methane and nitrogen) and chemical indicators (total nitrogen, total carbon, and total sulfate) were examined in five deep sediment cores (up to 130 m in length) obtained from the Hangzhou Bay. The V3-V4 region of the 16S rRNA gene amplicons was amplified and sequenced for the prokaryotic community analysis. The species composition, along with the physicochemical factors of the sediments, revealed a strong correlation with methane content in one of the sediment cores. We then obtained metagenomes of the two sediment samples selected for their high methane content and enrichment of methanogenic Bathyarchaeota with phylogenetic evidence. A total of 27 draft genomes were retrieved through metagenomic binning methodologies and were classified into Bathyarchaeota, Asgard archaea, Planctomycetes, and other microbial groups. The data provided are valuable for understanding the relationship between methane generation and microbial community composition in deep sediment core samples from coastal to marine environments.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Microbiota
*Metagenome
*Archaea/genetics
*RNA, Ribosomal, 16S/genetics
Phylogeny