@article {pmid39267516,
year = {2024},
author = {Liu, YZ and Zhang, R and Xie, JJ and Guo, Q and Zhan, CX and Chen, MY and Li, JS and Peng, XM},
title = {[Two cases of neonatal Legionella pneumonia].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {26},
number = {9},
pages = {986-988},
pmid = {39267516},
issn = {1008-8830},
mesh = {Humans ; Female ; Infant, Newborn ; *Legionnaires' Disease/diagnosis/drug therapy ; },
abstract = {Patient 1, a 12-day-old female infant, presented with fever, cough, dyspnea, and elevated infection markers, requiring respiratory support. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid revealed Legionella pneumophila (LP), leading to diagnoses of LP pneumonia and LP sepsis. The patient was treated with erythromycin for 15 days and azithromycin for 5 days, resulting in recovery and discharge. Patient 2, an 11-day-old female infant, presented with dyspnea, fever, elevated infection markers, and multiple organ dysfunction, requiring mechanical ventilation. mNGS of blood and cerebrospinal fluid indicated LP, leading to diagnoses of LP pneumonia, LP sepsis, and LP intracranial infection. The patient was treated with erythromycin for 19 days and was discharged after recovery. Neonatal LP pneumonia lacks specific clinical symptoms, and azithromycin is the preferred antimicrobial agent. The use of mNGS can provide early and definitive diagnosis for severe neonatal pneumonia of unknown origin.},
}

Humans
Female
Infant, Newborn
*Legionnaires' Disease/diagnosis/drug therapy

@article {pmid39267333,
year = {2024},
author = {Fujii, N and Kuroda, K and Narihiro, T and Aoi, Y and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e70007},
doi = {10.1111/1758-2229.70007},
pmid = {39267333},
issn = {1758-2229},
support = {23KJ16420A//JSPS KAKENHI/ ; JP16H04833//JSPS KAKENHI/ ; JP20H02287//JSPS KAKENHI/ ; },
mesh = {*Sewage/microbiology ; *Symbiosis ; *Zoogloea/genetics/metabolism ; *Wastewater/microbiology ; In Situ Hybridization, Fluorescence ; Metagenome ; Phylogeny ; },
abstract = {Candidatus Patescibacteria, also known as candidate phyla radiation (CPR), including the class-level uncultured clade JAEDAM01 (formerly a subclass of Gracilibacteria/GN02/BD1-5), are ubiquitous in activated sludge. However, their characteristics and relationships with other organisms are largely unknown. They are believed to be episymbiotic, endosymbiotic or predatory. Despite our understanding of their limited metabolic capacity, their precise roles remain elusive due to the difficulty in cultivating and identifying them. In previous research, we successfully recovered high-quality metagenome-assembled genomes (MAGs), including a member of JAEDAM01 from activated sludge flocs. In this study, we designed new probes to visualize the targeted JAEDAM01-associated MAG HHAS10 and identified its host using fluorescence in situ hybridization (FISH). The FISH observations revealed that JAEDAM01 HHAS10-like cells were located within dense clusters of Zoogloea, and the fluorescence brightness of zoogloeal cells decreased in the vicinity of the CPR cells. The Zoogloea MAGs possessed genes related to extracellular polymeric substance biosynthesis, floc formation and nutrient removal, including a polyhydroxyalkanoate (PHA) accumulation pathway. The JAEDAM01 MAG HHAS10 possessed genes associated with type IV pili, competence protein EC and PHA degradation, suggesting a Zoogloea-dependent lifestyle in activated sludge flocs. These findings indicate a new symbiotic relationship between JAEDAM01 and Zoogloea.},
}

*Sewage/microbiology
*Symbiosis
*Zoogloea/genetics/metabolism
*Wastewater/microbiology
In Situ Hybridization, Fluorescence
Metagenome
Phylogeny

@article {pmid39267241,
year = {2024},
author = {Doni, L and Azzola, A and Oliveri, C and Bosi, E and Auguste, M and Morri, C and Bianchi, CN and Montefalcone, M and Vezzulli, L},
title = {Genome-resolved metagenomics revealed novel microbial taxa with ancient metabolism from macroscopic microbial mat structures inhabiting anoxic deep reefs of a Maldivian Blue Hole.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e13315},
doi = {10.1111/1758-2229.13315},
pmid = {39267241},
issn = {1758-2229},
support = {CN_00000033//Centro Nazionale di Ricerca - Biodiversità (Italy) project (PNRR CN00000033 - Centro Nazionale Biodiversità/ ; CUP D33C22000960007//Italian Ministry of University and Research/ ; },
mesh = {*Metagenomics ; *Phylogeny ; *Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Geologic Sediments/microbiology ; Genome, Bacterial/genetics ; Anaerobiosis ; Deltaproteobacteria/genetics/classification/isolation & purification/metabolism ; Chloroflexi/genetics/classification/isolation & purification/metabolism ; Proteobacteria/genetics/classification/isolation & purification ; Microbiota ; },
abstract = {Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments.},
}

*Metagenomics
*Phylogeny
*Metagenome
Bacteria/classification/genetics/isolation & purification/metabolism
Geologic Sediments/microbiology
Genome, Bacterial/genetics
Anaerobiosis
Deltaproteobacteria/genetics/classification/isolation & purification/metabolism
Chloroflexi/genetics/classification/isolation & purification/metabolism
Proteobacteria/genetics/classification/isolation & purification
Microbiota

@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13881},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}

@article {pmid39275258,
year = {2024},
author = {Wang, M and Chen, Y and Song, AX and Weng, X and Meng, Y and Lin, J and Mao, YH},
title = {The Combination of Exercise and Konjac Glucomannan More Effectively Prevents Antibiotics-Induced Dysbiosis in Mice Compared with Singular Intervention.},
journal = {Nutrients},
volume = {16},
number = {17},
pages = {},
pmid = {39275258},
issn = {2072-6643},
support = {2023A1515010004//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZDZX2035//Special Funds in Key Areas of Guangdong Provincial Department of Education/ ; S202410585045//The College Students Innovation and Entrepreneurship Training Program/ ; 202410585015//The College Students Innovation and Entrepreneurship Training Program/ ; 82003434//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Mannans/pharmacology ; *Dysbiosis/prevention & control/chemically induced ; *Mice, Inbred C57BL ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Physical Conditioning, Animal ; Mice ; Male ; Combined Modality Therapy ; },
abstract = {Our previous studies have demonstrated that konjac glucomannan (KGM) can prevent dysbiosis induced by antibiotics. While exercise may also impact the gut microbiome, there are limited studies reporting its protective effect on antibiotic-induced dysbiosis. Therefore, this study investigated the preventive and regulatory effects of a combination of 6-week exercise and KGM intervention on antibiotic-induced dysbiosis in C57BL/6J mice compared with a single intervention. The results showed that combined exercise and KGM intervention could restore the changes in the relative abundance of Bacteroides (3.73% with CTL versus 14.23% with ATBX versus 4.46% with EK) and Prevotellaceae_Prevotella (0.33% with CTL versus 0.00% with ATBX versus 0.30% with EK) induced by antibiotics (p < 0.05), and minimized the Bray-Curtis distance induced by antibiotics (0.55 with CTL versus 0.81 with ATBX versus 0.80 with EXC versus 0.83 with KGM versus 0.75 with EK). Compared with the combined intervention, exercise intervention also produced a certain level of recovery effects; the relative abundance of Rikenellaceae (1.96% with CTL versus 0.09% with ATBX versus 0.49% with EXC) was restored, while KGM supplementation showed the best preventive effect. In addition, the combination of exercise and KGM significantly enriched microbial purine metabolic pathways (p < 0.05). These findings indicate that combining exercise with KGM could be a promising approach to reducing the side effects of antibiotics on the gut microbiome.},
}

Animals
*Mannans/pharmacology
*Dysbiosis/prevention & control/chemically induced
*Mice, Inbred C57BL
*Anti-Bacterial Agents/pharmacology/adverse effects
*Gastrointestinal Microbiome/drug effects
*Physical Conditioning, Animal
Mice
Male
Combined Modality Therapy

@article {pmid39274545,
year = {2024},
author = {Dera, N and Żeber-Lubecka, N and Ciebiera, M and Kosińska-Kaczyńska, K and Szymusik, I and Massalska, D and Dera, K and Bubień, K},
title = {Intrauterine Shaping of Fetal Microbiota.},
journal = {Journal of clinical medicine},
volume = {13},
number = {17},
pages = {},
pmid = {39274545},
issn = {2077-0383},
abstract = {Mechanisms resulting from the physiological immaturity of the digestive system in children delivered before 32 weeks of gestation and, in particular, different interactions between the microbiome and the body have not been fully elucidated yet. Next-generation sequencing methods demonstrated the presence of bacterial DNA in the placenta and amniotic fluid, which may reflect bacterial populations that initiate intestinal colonization in utero. Numerous studies confirmed the hypothesis stating that intestinal bacteria played an important role in the pathogenesis of necrotizing enterocolitis (NEC) early- and late-onset neonatal sepsis (EONS and LONS). The model and scale of disorders within the intestinal microbiome are the subject of active research in premature infants. Neonatal meconium was primarily used as an indicator defining the environment in utero, as it is formed before birth. Metagenomic results and previous data from microbiological bacterial cultures showed a correlation between the time from birth to sample collection and the detection of bacteria in the neonatal meconium. Therefore, it may be determined that the colonization of the newborn's intestines is influenced by numerous factors, which may be divided into prenatal, perinatal, and postnatal, with particular emphasis put on the mode of delivery and contact with the parent immediately after birth. Background: The aim of this review was to collect available data on the intrauterine shaping of the fetal microbiota. Methods: On 13 March 2024, the available literature in the PubMed National Library of Medicine search engine was reviewed using the following selected keywords: "placental microbiome", "intestinal bacteria in newborns and premature infants", and "intrauterine microbiota". Results: After reviewing the available articles and abstracts and an in-depth analysis of their content, over 100 articles were selected for detailed elaboration. We focused on the origin of microorganisms shaping the microbiota of newborns. We also described the types of bacteria that made up the intrauterine microbiota and the intestinal microbiota of newborns. Conclusions: The data presented in the review on the microbiome of both term newborns and those with a body weight below 1200 g indicate a possible intrauterine colonization of the fetus depending on the duration of pregnancy. The colonization occurs both via the vaginal and intestinal route (hematogenous route). However, there are differences in the demonstrated representatives of various types of bacteria, phyla Firmicutes and Actinobacteria in particular, taking account of the distribution in their abundance in the individual groups of pregnancy duration. Simultaneously, the distribution of the phyla Actinobacteria and Proteobacteria is consistent. Considering the duration of pregnancy, it may also be concluded that the bacterial flora of vaginal origin dominates in preterm newborns, while the flora of intestinal origin dominates in term newborns. This might explain the role of bacterial and infectious factors in inducing premature birth with the rupture of fetal membranes.},
}

@article {pmid39273435,
year = {2024},
author = {Di Chiano, M and Sallustio, F and Fiocco, D and Rocchetti, MT and Spano, G and Pontrelli, P and Moschetta, A and Gesualdo, L and Gadaleta, RM and Gallone, A},
title = {Psychobiotic Properties of Lactiplantibacillus plantarum in Neurodegenerative Diseases.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273435},
issn = {1422-0067},
support = {1062//PON "RICERCA E INNOVAZIONE" 2014-2020-Innovazione/ ; Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - Next Generation EU//National Recovery and Resilience Plan (NRRP)/ ; Concession Decree No. 1550 of 11 October 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001//Italian Ministry of University and Research, CUP D93C22000890001/ ; Codice progetto n. 2022H9MPZ5//MIUR- PRIN Progetti di Ricerca di Rilevante Interesse Nazionale 2022/ ; Id. 23239//AIRC IG 2019/ ; Call for tender No. 3138 of 16/12/2021 of Italian Ministry of University and Research funded by the European Union//National Recovery and Resilience Plan (NRRP)/ ; Project code: CN00000041, CUP H93C22000430007//NextGenerationEU/ ; PNRR-MR1-2022-12376395//European Union - Next Generation EU - PNRR M6C2/ ; "POFACS" - ARS01_00640 -", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MIUR)/ ; PRA-HE 2021//University of Foggia/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/microbiology ; Brain-Gut Axis ; Animals ; },
abstract = {Neurodegenerative disorders are the main cause of cognitive and physical disabilities, affect millions of people worldwide, and their incidence is on the rise. Emerging evidence pinpoints a disturbance of the communication of the gut-brain axis, and in particular to gut microbial dysbiosis, as one of the contributors to the pathogenesis of these diseases. In fact, dysbiosis has been associated with neuro-inflammatory processes, hyperactivation of the neuronal immune system, impaired cognitive functions, aging, depression, sleeping disorders, and anxiety. With the rapid advance in metagenomics, metabolomics, and big data analysis, together with a multidisciplinary approach, a new horizon has just emerged in the fields of translational neurodegenerative disease. In fact, recent studies focusing on taxonomic profiling and leaky gut in the pathogenesis of neurodegenerative disorders are not only shedding light on an overlooked field but are also creating opportunities for biomarker discovery and development of new therapeutic and adjuvant strategies to treat these disorders. Lactiplantibacillus plantarum (LBP) strains are emerging as promising psychobiotics for the treatment of these diseases. In fact, LBP strains are able to promote eubiosis, increase the enrichment of bacteria producing beneficial metabolites such as short-chain fatty acids, boost the production of neurotransmitters, and support the homeostasis of the gut-brain axis. In this review, we summarize the current knowledge on the role of the gut microbiota in the pathogenesis of neurodegenerative disorders with a particular focus on the benefits of LBP strains in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, autism, anxiety, and depression.},
}

Humans
*Neurodegenerative Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
Dysbiosis/microbiology
Brain-Gut Axis
Animals

@article {pmid39273328,
year = {2024},
author = {Zhu, N and Qian, Y and Song, L and Yu, Q and Sheng, H and Li, Y and Zhu, X},
title = {Regulating Leaf Photosynthesis and Soil Microorganisms through Controlled-Release Nitrogen Fertilizer Can Effectively Alleviate the Stress of Elevated Ambient Ozone on Winter Wheat.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273328},
issn = {1422-0067},
support = {BE2022312//Special Technology Innovation Fund of Carbon Neutrality in Jiangsu Province/ ; },
mesh = {*Fertilizers ; *Triticum/growth & development/metabolism/microbiology/drug effects ; *Photosynthesis/drug effects ; *Soil Microbiology ; *Plant Leaves/drug effects/metabolism ; *Nitrogen/metabolism ; *Ozone/pharmacology ; Stress, Physiological ; Soil/chemistry ; Bacteria/drug effects/metabolism/genetics ; },
abstract = {The mitigation mechanisms of a kind of controlled-release nitrogen fertilizer (sulfur-coated controlled-release nitrogen fertilizer, SCNF) in response to O3 stress on a winter wheat (Triticum aestivum L.) variety (Nongmai-88) were studied in crop physiology and soil biology through the ozone-free-air controlled enrichment (O3-FACE) simulation platform and soil microbial metagenomics. The results showed that SCNF could not delay the O3-induced leaf senescence of winter wheat but could enhance the leaf size and photosynthetic function of flag leaves, increase the accumulation of nutrient elements, and lay the foundation for yield by regulating the release rate of nitrogen (N). By regulating the soil environment, SCNF could maintain the diversity and stability of soil bacterial and archaeal communities, but there was no obvious interaction with the soil fungal community. By alleviating the inhibition effects of O3 on N-cycling-related genes (ko00910) of soil microorganisms, SCNF improved the activities of related enzymes and might have great potential in improving soil N retention. The results demonstrated the ability of SCNF to improve leaf photosynthetic function and increase crop yield under O3-polluted conditions in the farmland ecosystem, which may become an effective nitrogen fertilizer management measure to cope with the elevated ambient O3 and achieve sustainable production.},
}

*Fertilizers
*Triticum/growth & development/metabolism/microbiology/drug effects
*Photosynthesis/drug effects
*Soil Microbiology
*Plant Leaves/drug effects/metabolism
*Nitrogen/metabolism
*Ozone/pharmacology
Stress, Physiological
Soil/chemistry
Bacteria/drug effects/metabolism/genetics

@article {pmid39273112,
year = {2024},
author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T},
title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273112},
issn = {1422-0067},
mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Metagenome ; },
abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.},
}

Female
Animals
Pregnancy
*RNA, Ribosomal, 16S/genetics
Cattle
*Postpartum Period
*Vagina/microbiology
*Microbiota/genetics
*Uterus/microbiology
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Metagenome

@article {pmid39271469,
year = {2024},
author = {Ciuchcinski, K and Stokke, R and Steen, IH and Dziewit, L},
title = {Landscape of the Metaplasmidome of Deep-Sea Hydrothermal Vents located at Arctic Mid-Ocean Ridges in the Norwegian-Greenland Sea - Ecological Insights from Comparative Analysis of Plasmid Identification Tools.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae124},
pmid = {39271469},
issn = {1574-6941},
abstract = {Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools - PlasX, GeNomad and PLASMe - on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multi-approach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analyzing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.},
}

@article {pmid39271424,
year = {2024},
author = {Bokulich, NA and Robeson, MS},
title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.08.011},
pmid = {39271424},
issn = {1878-4380},
abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.},
}

@article {pmid39094785,
year = {2024},
author = {Dhakal, U and Yue, W and Leslie, JF and Toomajian, C},
title = {Population genomics of Fusarium graminearum isolates from the Americas.},
journal = {Fungal genetics and biology : FG & B},
volume = {174},
number = {},
pages = {103924},
doi = {10.1016/j.fgb.2024.103924},
pmid = {39094785},
issn = {1096-0937},
mesh = {*Fusarium/genetics/classification/isolation & purification ; *Plant Diseases/microbiology ; *Polymorphism, Single Nucleotide/genetics ; *Linkage Disequilibrium ; Triticum/microbiology ; Genome, Fungal/genetics ; Americas ; Genotype ; Genomics ; Metagenomics ; Hordeum/microbiology ; Uruguay ; },
abstract = {Fusarium head blight (FHB) is a major disease of wheat and barley worldwide and is caused by different species in the genus Fusarium, Fusarium graminearum being the most important. We conducted population genomics analyses using SNPs obtained through genotyping by sequencing of over 500 isolates of F. graminearum from the US Upper Midwest, New York, Louisiana, and Uruguay. PCA and STRUCTURE analyses group our isolates into four previously described populations: NA1, NA2, Southern Louisiana (SLA) and Gulf Coast (GC). Some isolates were not assigned to populations because of mixed ancestry. Population structure was associated with toxin genotype and geographic origin. The NA1, NA2, and SLA populations are differentiated (FST 0.385 - 0.551) but the presence of admixed isolates indicates that the populations are not reproductively isolated. Patterns of linkage disequilibrium (LD) decay suggest frequent recombination within populations. Fusarium graminearum populations from the US have great evolutionary potential given the high recombination rate and a large proportion of admixed isolates. The NA1, NA2, and Southern Louisiana (SLA) populations separated from their common ancestral population roughly at the same time in the past and are evolving with moderate levels of subsequent gene flow between them. Genome-wide selection scans in all three populations revealed outlier regions with the strongest signatures of recent positive natural selection. These outlier regions include many genes with unknown function and some genes with known roles in plant-microbe interaction, fungicide/drug resistance, cellular transport and genes that are related to cellular organelles. Only a very small proportion of outlier regions are shared as outliers among the three populations, suggesting unique host-pathogen interactions and environmental adaptation.},
}

*Fusarium/genetics/classification/isolation & purification
*Plant Diseases/microbiology
*Polymorphism, Single Nucleotide/genetics
*Linkage Disequilibrium
Triticum/microbiology
Genome, Fungal/genetics
Americas
Genotype
Genomics
Metagenomics
Hordeum/microbiology
Uruguay

@article {pmid39271095,
year = {2024},
author = {do Socorro Foro Ramos, E and Barbosa, MRF and Villanova, F and Silva, RLO and Garcia, SC and Mendes-Correa, MC and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E},
title = {Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105668},
doi = {10.1016/j.meegid.2024.105668},
pmid = {39271095},
issn = {1567-7257},
abstract = {The global challenge of water resource availability is exacerbated by anthropogenic influences that promote the emergence of pollutants. Among these pollutants are microbiological agents, including viruses, which are ubiquitous in the biosphere and play a pivotal role in both ecological balance and the occurrence of diseases in animals and plants. Consequently, monitoring viruses in water sources becomes indispensable for the establishment of effective prevention, promotion, and control strategies. Within this context, the study focuses on the identification of novel viruses belonging to the Picornavirales order in freshwater from the Guarapiranga Reservoir in the state of São Paulo, Brazil. The samples were subjected to viral metagenomics. Our analysis led to the characterization of four distinct sequences (GinkV-05, AquaV_10, MarV_14, and MarV_64), which exhibited significant divergence compared to other members of the Picornavirales order. This remarkable diversity prompted the identification of a potential new genus within the Marnaviridae family, tentatively named Ginkgonavirus. Additionally, we characterized four sequences in a very distinct clade and propose the recognition of a novel family (named Aquaviridae) within the Picornavirales order. Our findings contribute valuable insights into the previously uncharted diversity of Picornavirales present in water sources, shedding light on an important facet of viral ecology and evolution in aquatic environments.},
}

@article {pmid39271075,
year = {2024},
author = {Xu, X and Chen, H and Du, L and Deng, C and Ma, R and Li, B and Li, J and Liu, S and Karthikeyan, R and Chen, Q and Sun, W},
title = {Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143332},
doi = {10.1016/j.chemosphere.2024.143332},
pmid = {39271075},
issn = {1879-1298},
abstract = {Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.},
}

@article {pmid39270978,
year = {2024},
author = {Fang, Z and Zang, Q and Chen, J and Li, Z and Yang, D and Wu, C and Yang, H and Guo, N},
title = {Whole-body mass spectrometry imaging reveals the systemic metabolic disorder and catecholamines biosynthesis alteration on heart-gut axis in heart failure rat.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.09.001},
pmid = {39270978},
issn = {2090-1224},
abstract = {INTRODUCTION: Heart failure (HF) is a systemic metabolic disorder disease, across multiorgan investigations advancing knowledge of progression and treatment of HF. Whole-body MSI provides spatiotemporal information of metabolites in multiorgan and is expected to be a potent tool to dig out the complex mechanism of HF.

OBJECTIVES: This study aimed at exploring the systemic metabolic disorder in multiorgan and catecholamines biosynthesis alteration on heart-gut axis after HF.

METHODS: Whole-body MSI was used to characterize metabolic disorder of the whole rat body after HF. An integrated method by MSI, LC-MS/MS and ELISA was utilized to analyze key metabolites and enzymes on heart, small intestine, cecum and colon tissues of rat. Gut microbiota dysbiosis was investigated by 16S rDNA sequencing and metagenomic sequencing. Validation experiments and in vitro experiments were performed to verify the effect of catecholamines biosynthesis alteration on heart-gut axis after HF.

RESULTS: Whole-body MSI exhibited varieties of metabolites alteration in multiple organs. Remarkably, Catecholamine biosynthesis was significantly altered in the serum, heart and intestines of rats. Furthermore, catecholamines and tyrosine hydroxylase were obviously upregulated in heart and colon tissue. Turicibacter_sanguinis was relevant to catecholamines of heart and colon. Validation experiments demonstrated excessive norepinephrine induced cardio-intestinal injury, including significantly elevating the levels of BNP, pro-BNP, LPS, DAO, and increased the abundance of Turicibacter_sanguinis. These alterations could be reversed by metoprolol treatment blocking the effect of norepinephrine. Additionally, in vitro studies demonstrated that norepinephrine promoted the growth of Turicibacter_sanguinis and Turicibacter_sanguinis could import and metabolize norepinephrine. Collectively, excessive norepinephrine exerted bidirectional effects on cardio-intestinal function to participate in the progression of HF.

CONCLUSION: Our study provides a new approach to elucidate multiorgan metabolic disorder and proposes new insights into heart-gut axis in HF development.},
}

@article {pmid39270881,
year = {2024},
author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J},
title = {The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118816},
doi = {10.1016/j.jep.2024.118816},
pmid = {39270881},
issn = {1872-7573},
abstract = {The prevalence of allergic airway inflammation (AAI) worldwide is high. Artemisia annua L. pollen is spread worldwide, and allergic diseases caused by its plant polysaccharides, which are closely related to the intestinal microbiota, have anti-inflammatory effects. Further isolation and purification of Lycium barbarum L. yielded its most effective component Lycium barbarum L. glycopeptide (LbGP), which can inhibit inflammation in animal models. However, its therapeutic effect on AAI and its mechanism of regulating the intestinal flora have not been fully investigated.

AIM OF THE STUDY: To explore LbGP in APE-induced immunological mechanisms of AAI and the interaction mechanism of the intestinal flora and metabolites.

METHODS: A mouse model of AAI generated from Artemisia annua pollen was constructed, and immunological indices related to the disease were examined. A combination of macrogenomic and metabolomic analyses was used to investigate the effects of LbGP on the gut microbial and metabolite profiles of mice with airway inflammation.

RESULTS: LbGP effectively alleviated Artemisia. annua pollen extract (APE)-induced AAI, corrected Th1/Th2 immune dysregulation, decreased Th17 cells, increased Treg cells, and altered the composition and function of the intestinal microbiota. LbGP treatment increased the number of Odoribacter, Duncaniella, Ruminococcus, and Alistipes in the intestines of the mice, but the numble of Alistipes decreased. Macrogenomic functional analysis and metabolite pathway enrichment analysis were used to determine the effects of taurine and hypotaurine metabolism, bile acid secretion, and pyrimidine metabolism pathways on disease.

CONCLUSION: Our results revealed significant changes in the macrogenome and metabolome following APE and LbGP intervention, revealed potential correlations between gut microbial species and metabolites, and highlighted the beneficial effects of LbGP on AAI through the modulation of the gut microbiome and host metabolism.},
}

@article {pmid39270504,
year = {2024},
author = {Deng, J and Kang, D and Zhang, Y and Chen, B and Xia, C and Yu, C and Peng, Y},
title = {Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen.},
journal = {Water research},
volume = {266},
number = {},
pages = {122420},
doi = {10.1016/j.watres.2024.122420},
pmid = {39270504},
issn = {1879-2448},
abstract = {Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.},
}

@article {pmid39270468,
year = {2024},
author = {Erdemir, F and Karabulut, A and Aydin, U and Guler, S and Cicek, A and Gokduman, SN and Eser, E and Birdogan, S and Kocagoz, T},
title = {Metagenomic analysis of atheroma plaques for identification of microorganisms indicates presence of Toxoplasma gondii as a possible etiological agent.},
journal = {Journal of infection and public health},
volume = {17},
number = {10},
pages = {102539},
doi = {10.1016/j.jiph.2024.102539},
pmid = {39270468},
issn = {1876-035X},
abstract = {BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Vital organs like the heart are affected by the occlusion of blood vessels due to atherosclerotic plaque formation. However, the role of infectious agents has always been an essential subject of investigation. This study investigated the presence of microorganisms, including nanobacteria, in atherosclerotic plaques removed from human carotid arteries by microbiological and metagenomic examination.

METHODS: Atheroma plaque samples were obtained from 20 patients with carotid artery stenosis who had atherectomy by surgery or percutaneous intervention. Nanobacteria were grown by culturing homogenates of the atheroma plaques. Whole genome sequencing was done for samples. Because of the high percentage of Toxoplasma gondii (T. gondii) DNA, PCR investigation was applied to detect T. gondii DNA in the samples.

RESULTS: A molecular analysis of nanobacteria revealed them to be made of human proteins, supporting the theory that they are not living organisms. According to sequencing results, samples showed that more than 50 % of the metagenomic sequences belonged to Toxoplasma gondii. PCR investigation indicated that T. gondii DNA was positive in 8 (40 %) of 20 plaques.

CONCLUSIONS: Further evidence regarding the role of T. gondii in the etiology of plaque formation may help determine the strategy for prevention and treatment of infections in preventing atheroma plaque formation in the future.},
}

@article {pmid39269181,
year = {2024},
author = {Quan, Q and Liu, J and Li, C and Ke, Z and Tan, Y},
title = {Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054924},
doi = {10.1128/msphere.00549-24},
pmid = {39269181},
issn = {2379-5042},
abstract = {UNLABELLED: Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms.

IMPORTANCE: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.},
}

@article {pmid39268953,
year = {2024},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Zhu, R and Wang, H},
title = {Identification of a Novel Parvovirus in the Arctic Wolf (Canis lupus arctos).},
journal = {Polish journal of microbiology},
volume = {73},
number = {3},
pages = {395-401},
pmid = {39268953},
issn = {2544-4646},
mesh = {Animals ; *Phylogeny ; *Genome, Viral ; *Wolves/virology ; *Open Reading Frames ; *Parvovirus/genetics/classification/isolation & purification ; Capsid Proteins/genetics ; Parvoviridae Infections/virology/veterinary ; Base Composition ; China ; DNA, Viral/genetics ; },
abstract = {A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.},
}

Animals
*Phylogeny
*Genome, Viral
*Wolves/virology
*Open Reading Frames
*Parvovirus/genetics/classification/isolation & purification
Capsid Proteins/genetics
Parvoviridae Infections/virology/veterinary
Base Composition
China
DNA, Viral/genetics

@article {pmid39268488,
year = {2024},
author = {Hu, L and Huang, X and Yee, NH and Meng, H and Jiang, L and Liang, L and Chen, X},
title = {Pythium insidiosum: an emerging pathogen that is easily misdiagnosed and given treatment as a fungus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1430032},
pmid = {39268488},
issn = {2235-2988},
mesh = {*Pythium/isolation & purification/drug effects/genetics ; Humans ; *Pythiosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/pharmacology/therapeutic use ; *Microbial Sensitivity Tests ; Male ; Diagnostic Errors ; Communicable Diseases, Emerging/microbiology/diagnosis/drug therapy ; Keratitis/microbiology/diagnosis/drug therapy ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Aged ; },
abstract = {BACKGROUND: Pythium insidiosum (P. insidiosum) is the causative agent of pythiosis, an infectious disease with a high morbidity and fatality rate. Pythiosis cases have increased dramatically during the past ten years, particularly in tropical and subtropical areas. Sadly, microbiologists and medical professionals know very little about pythiosis, and the disease is frequently challenging to identify. It is frequently misdiagnosed as a fungal infection.

METHODS: We report two cases of pythiosis, one was Pythium keratitis, the other was cutaneous pythiosis. The patient with corneal infection had no underlying disease, while the patient with cutaneous pythiosis had a history of liver cirrhosis, diabetes, and psoriasis. The corneal sample and subcutaneous pus were sent for metagenomic Next-Generation Sequencing (mNGS). To further diagnose the isolated strain, P. insidiosum zoospores were induced to produce by co-incubation with sterile grass leaves in sterile pond water. Their zoospores were used as an inoculum for drug susceptibility testing by disk diffusion and broth microdilution method.

RESULTS: The mNGS of two cases were reported as P. insidiosum. Zoospores were produced after incubation 48h. The zoospores were collected for drug susceptibility assay. All antifungal drugs, antibacterial drugs of β-Lactams, vancomycin, levofloxacin, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole, clindamycin have no inhibitory activity against P. insidiosum in vitro. Minocycline, tigecycline, linezolid, erythromycin and azithromycin have significant in vitro activity against P. insidiosum. Based on the susceptibility results, the drug was changed from itraconazole to linezolid and minocycline, along with multiple debridements and drainage for cutaneous pythiosis. The patient was discharged after 24 days of treatment.

CONCLUSIONS: Early and accurate identification, combined with aggressive surgical debridement and appropriate drug therapy, can greatly improve patient managements. Conventional culture and zoospore induction remain gold standard for diagnosis; however, DNA-based method should be performed simultaneously. The drug susceptibility testing provides profound effects on proper drug selection against P. insidiosum.},
}

*Pythium/isolation & purification/drug effects/genetics
Humans
*Pythiosis/diagnosis/microbiology/drug therapy
*Antifungal Agents/pharmacology/therapeutic use
*Microbial Sensitivity Tests
Male
Diagnostic Errors
Communicable Diseases, Emerging/microbiology/diagnosis/drug therapy
Keratitis/microbiology/diagnosis/drug therapy
Middle Aged
High-Throughput Nucleotide Sequencing
Female
Aged

@article {pmid39268238,
year = {2024},
author = {Wang, J and Su, C and Qian, M and Wang, X and Chen, C and Liu, Y and Liu, W and Xiang, Z and Xu, B},
title = {Subchronic toxic effects of bisphenol A on the gut-liver-hormone axis in rats via intestinal flora and metabolism.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1415216},
pmid = {39268238},
issn = {1664-2392},
mesh = {Animals ; *Phenols/toxicity ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Benzhydryl Compounds/toxicity ; *Liver/drug effects/metabolism/pathology ; *Endocrine Disruptors/toxicity ; Rats, Sprague-Dawley ; Hormones/blood ; },
abstract = {BACKGROUND: Bisphenol A (BPA), a characteristic endocrine disruptor, is a substance that seriously interferes with the human endocrine system and causes reproductive disorders and developmental abnormalities. However, its toxic effects on the gut-liver-hormone axis are still unclear.

METHOD: Male and female rats were exposed to BPA (300 mg/kg) by oral gavage for 60 consecutive days. H&E staining was used for histopathological evaluation, and the serum biochemical indexes were determined using an automatic analyzer. The 16S rRNA gene sequencing was used to detect the intestinal microbial diversity, and the GC-MS was used to analyze the contents of short-chain fatty acids (SCFAs) in colon contents. UPLC-QTOF MS was used to analyze the related metabolites. The ELISA method was used to assess the levels of serum inflammatory factors.

RESULTS: Histopathological analysis indicated that the liver, heart, and testis were affected by BPA. There was a significant effect on alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL) in the male-BPA group (P < 0.05), and globulin (GLB), indirect bilirubin (IBIL), alkaline phosphatase (ALP), ALT, TG, TC, high-density lipoprotein (HDL), and creatinine (Cr) in the female-BPA group (P < 0.05). Metagenomics (16S rRNA gene sequencing) analysis indicated that BPA reduced the diversity and changed the composition of gut microbiota in rats significantly. Compared with the control and blank groups, the contents of caproic acid, isobutyric acid, isovaleric acid, and propanoic acid in the colon contents decreased in the male-BPA group (P < 0.05), and caproic acid, isobutyric acid, isovaleric acid, and valeric acid in the colon contents decreased in the female-BPA group (P < 0.05). Metabolomic analysis of the serum indicated that BPA could regulate bile acid levels, especially ursodeoxycholic acid (UDCA) and its conjugated forms. The contents of amino acids, hormones, and lipids were also significantly affected after exposure to BPA. The increase in interleukin-6 (IL-6), interleukin-23 (IL-23), and transforming growth factor-β (TGF-β) in the serum of the male-BPA group suggests that BPA exposure affects the immune system.

CONCLUSION: BPA exposure will cause toxicity to rats via disrupting the gut-liver-hormone axis.},
}

Animals
*Phenols/toxicity
Male
Female
Rats
*Gastrointestinal Microbiome/drug effects
*Benzhydryl Compounds/toxicity
*Liver/drug effects/metabolism/pathology
*Endocrine Disruptors/toxicity
Rats, Sprague-Dawley
Hormones/blood

@article {pmid39268134,
year = {2024},
author = {Liu, X and Zhao, Q and He, X and Min, J and Yao, RSY and Chen, Z and Ma, J and Hu, W and Huang, J and Wan, H and Guo, Y and Zhou, M},
title = {Clinical characteristics and microbial signatures in the lower airways of diabetic and nondiabetic patients with pneumonia.},
journal = {Journal of thoracic disease},
volume = {16},
number = {8},
pages = {5262-5273},
pmid = {39268134},
issn = {2072-1439},
abstract = {BACKGROUND: The microbial signatures in diabetes with pneumonia and the risk factors of severe pneumonia (SP) in diabetic patients are not clear. Our study explored microbial signatures and the association between clinical characteristics and SP then constructed a risk model to find effective biomarkers for predicting pneumonia severity.

METHODS: Our study was conducted among 273 patients with pneumonia diagnosed and treated in our hospital from January 2018 to May 2021. Bronchoalveolar lavage fluid (BALF) samples and clinical data were collected. Metagenomic sequencing was applied after extracting the DNA from samples. Appropriate statistical methods were used to compare the microbial signatures and clinical characteristics in patients with or without diabetes mellitus (DM).

RESULTS: In total, sixty-one pneumonia patients with diabetes and 212 pneumonia patients without diabetes were included. Sixty-six differential microorganisms were found to be associated with SP in diabetic patients. Some microbes correlated with clinical indicators of SP. The prediction model for SP was established and the receiver operating characteristic (ROC) curve demonstrated its accuracy, with the sensitivity and specificity of 0.82 and 0.91, respectively.

CONCLUSIONS: Some microorganisms affect the severity of pneumonia. We identified the microbial signatures in the lower airways and the association between clinical characteristics and SP. The predictive model was more accurate in predicting SP by combining microbiological indicators and clinical characteristics, which might be beneficial to the early identification and management of patients with SP.},
}

@article {pmid39267171,
year = {2024},
author = {Gandasegui, J and Fleitas, PE and Petrone, P and Grau-Pujol, B and Novela, V and Rubio, E and Muchisse, O and Cossa, A and Jamine, JC and Sacoor, C and Brienen, EAT and van Lieshout, L and Muñoz, J and Casals-Pascual, C},
title = {Baseline gut microbiota diversity and composition and albendazole efficacy in hookworm-infected individuals.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {387},
pmid = {39267171},
issn = {1756-3305},
mesh = {*Albendazole/therapeutic use/pharmacology/administration & dosage ; Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anthelmintics/therapeutic use/administration & dosage ; *Hookworm Infections/drug therapy ; *Feces/parasitology/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Animals ; Young Adult ; Middle Aged ; Ancylostomatoidea/drug effects/genetics ; Adolescent ; Child ; },
abstract = {Soil-transmitted helminth (STH) infections account for a significant global health burden, necessitating mass drug administration with benzimidazole-class anthelmintics, such as albendazole (ALB), for morbidity control. However, ALB efficacy shows substantial variability, presenting challenges for achieving consistent treatment outcomes. We have explored the potential impact of the baseline gut microbiota on ALB efficacy in hookworm-infected individuals through microbiota profiling and machine learning (ML) techniques. Our investigation included 89 stool samples collected from hookworm-infected individuals that were analyzed by microscopy and quantitative PCR (qPCR). Of these, 44 were negative by microscopy for STH infection using the Kato-Katz method and qPCR 21 days after treatment, which entails a cure rate of 49.4%. Microbiota characterization was based on amplicon sequencing of the V3-V4 16S ribosomal RNA gene region. Alpha and beta diversity analyses revealed no significant differences between participants who were cured and those who were not cured, suggesting that baseline microbiota diversity does not influence ALB treatment outcomes. Furthermore, differential abundance analysis at the phylum, family and genus levels yielded no statistically significant associations between bacterial communities and ALB efficacy. Utilizing supervised ML models failed to predict treatment response accurately. Our investigation did not provide conclusive insights into the relationship between gut microbiota and ALB efficacy. However, the results highlight the need for future research to incorporate longitudinal studies that monitor changes in the gut microbiota related to the infection and the cure with ALB, as well as functional metagenomics to better understand the interaction of the microbiome with the drug, and its role, if there is any, in modulating anthelmintic treatment outcomes in STH infections. Interdisciplinary approaches integrating microbiology, pharmacology, genetics and data science will be pivotal in advancing our understanding of STH infections and optimizing treatment strategies globally.},
}

*Albendazole/therapeutic use/pharmacology/administration & dosage
Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Anthelmintics/therapeutic use/administration & dosage
*Hookworm Infections/drug therapy
*Feces/parasitology/microbiology
Female
Male
RNA, Ribosomal, 16S/genetics
Adult
Treatment Outcome
Animals
Young Adult
Middle Aged
Ancylostomatoidea/drug effects/genetics
Adolescent
Child

@article {pmid39267108,
year = {2024},
author = {Zheng, YR and Chen, XH and Chen, Q and Cao, H},
title = {Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study.},
journal = {Italian journal of pediatrics},
volume = {50},
number = {1},
pages = {174},
pmid = {39267108},
issn = {1824-7288},
mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; *Heart Defects, Congenital/surgery ; Infant ; *Metagenomics/methods ; *Cardiac Surgical Procedures/adverse effects ; Postoperative Complications/diagnosis ; Infant, Newborn ; Pneumonia/diagnosis/microbiology ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: This study aimed to compare targeted next-generation sequencing (tNGS) with metagenomic next-generation sequencing (mNGS) for pathogen detection in infants with severe postoperative pneumonia after congenital heart surgery.

METHODS: We conducted a retrospective observational study using data from the electronic medical record system of infants who developed severe pneumonia after surgery for congenital heart disease from August 2021 to August 2022. Infants were divided into tNGS and mNGS groups based on the pathogen detection methods. The primary outcome was the efficiency of pathogen detection, and the secondary outcomes were the timeliness and cost of each method.

RESULTS: In the study, 91 infants were included, with tNGS detecting pathogens in 84.6% (77/91) and mNGS in 81.3% (74/91) of cases (P = 0.55). No significant differences were found in sensitivity, specificity, PPA, and NPA between the two methods (P > 0.05). tNGS identified five strains with resistance genes, while mNGS detected one strain. Furthermore, tNGS had a faster detection time (12 vs. 24 h) and lower cost ($150 vs. $500) compared to mNGS.

CONCLUSION: tNGS offers similar sensitivity to mNGS but with greater efficiency and cost-effectiveness, making it a promising approach for respiratory pathogen detection.},
}

Humans
Retrospective Studies
*High-Throughput Nucleotide Sequencing
Male
Female
*Heart Defects, Congenital/surgery
Infant
*Metagenomics/methods
*Cardiac Surgical Procedures/adverse effects
Postoperative Complications/diagnosis
Infant, Newborn
Pneumonia/diagnosis/microbiology
Sensitivity and Specificity

@article {pmid39267031,
year = {2024},
author = {Liu, H and Ran, Q and Ma, J and Zhang, J and Tan, N and Xi, L and Li, X and Zhang, J and Lu, S},
title = {Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {84},
pmid = {39267031},
issn = {1476-0711},
support = {82172289//National Natural Science Foundation of China/ ; 202201020345//Guangzhou Municipal Science and Technology Project/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *Granuloma/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation & purification/genetics/classification ; Aged ; Sensitivity and Specificity ; Fungi/isolation & purification/genetics/classification ; Young Adult ; Metagenomics/methods ; Skin Diseases, Infectious/diagnosis/microbiology ; Adolescent ; Skin/microbiology/pathology ; Child ; },
abstract = {BACKGROUND: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished.

OBJECTIVE: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity.

METHODS: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS.

RESULTS: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS.

CONCLUSIONS: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.},
}

Humans
Retrospective Studies
Male
Female
Middle Aged
Adult
*Granuloma/microbiology/diagnosis
*High-Throughput Nucleotide Sequencing/methods
Bacteria/isolation & purification/genetics/classification
Aged
Sensitivity and Specificity
Fungi/isolation & purification/genetics/classification
Young Adult
Metagenomics/methods
Skin Diseases, Infectious/diagnosis/microbiology
Adolescent
Skin/microbiology/pathology
Child

@article {pmid39266944,
year = {2024},
author = {Meirelles, PM and Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP},
title = {Optimizing next-generation sequencing efficiency in clinical settings: analysis of read length impact on cost and performance.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {856},
pmid = {39266944},
issn = {1471-2164},
support = {2023-PPI-007//Rockefeller Foundation/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *COVID-19/virology ; Humans ; *SARS-CoV-2/genetics ; *Metagenomics/methods ; Bacteria/genetics ; },
abstract = {BACKGROUND: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification.

RESULTS: Our findings revealed that moving from 75 bp to 150 bp read length approximately doubles both the cost and sequencing time. Opting for 300 bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75 bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75 bp reads to 100% with 150-300 bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75 bp, 95% with 150 bp, and 97% with 300 bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa.

CONCLUSIONS: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75 bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability.},
}

*High-Throughput Nucleotide Sequencing/methods
*COVID-19/virology
Humans
*SARS-CoV-2/genetics
*Metagenomics/methods
Bacteria/genetics

@article {pmid39266528,
year = {2024},
author = {Liu, S and Chen, Q and Hou, C and Dong, C and Qiu, X and Tang, K},
title = {Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {994},
pmid = {39266528},
issn = {2052-4463},
mesh = {China ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics/classification ; Oxygen ; Seawater/microbiology ; Phylogeny ; Metagenomics ; Oceans and Seas ; Microbiota ; },
abstract = {The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.},
}

China
*Metagenome
*Archaea/genetics
Bacteria/genetics/classification
Oxygen
Seawater/microbiology
Phylogeny
Metagenomics
Oceans and Seas
Microbiota

@article {pmid39266450,
year = {2024},
author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C},
title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {Supplement_1},
pages = {},
doi = {10.1093/bib/bbae429},
pmid = {39266450},
issn = {1477-4054},
support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; },
mesh = {*Biofilms/growth & development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; },
abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.},
}

*Biofilms/growth & development
*Metagenomics/methods
Microbiota/genetics
Cloud Computing
Humans
Computational Biology/methods

@article {pmid39265854,
year = {2024},
author = {Viglioli, M and Mirjam Rizzo, S and Alessandri, G and Fontana, F and Milani, C and Turroni, F and Mancabelli, L and Croci, N and Rivara, S and Vacondio, F and Ventura, M and Mor, M},
title = {Investigating drug-gut microbiota interactions: Reductive and hydrolytic metabolism of oral glucocorticoids by in vitro artificial gut microbiota.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {124663},
doi = {10.1016/j.ijpharm.2024.124663},
pmid = {39265854},
issn = {1873-3476},
abstract = {Elucidation of the role of gut microbiota in the metabolism of orally administered drugs may improve therapeutic effectiveness and contribute to the development of personalized medicine. In this study, ten different artificial gut microbiota (AGM), obtained by culturing fecal samples in a continuous fermentation system, were challenged for their metabolizing capacity on a panel of six glucocorticoids selected from either prodrugs or drugs. Data from metabolic stability assays highlighted that, while the hydrolysis-mediated conversion of prodrugs to drugs represented only a minor metabolic pathway, significant differences in the stability of parent compounds and in their conversion rates to multiple reductive metabolites were obtained for the selected drugs. In the latter case, a taxonomic composition-dependent ability to convert parent drugs to metabolites was observed. Indeed, the artificial microbial communities dominated by the genus Bacteroides showed the maximal conversion of parent glucocorticoids to several metabolites. Furthermore, the effect of drugs on AGM was also evaluated through shallow shotgun sequencing and flow cytometry-based total bacterial cell count highlighting that these drugs can affect both the taxonomic composition and growth performances of the human gut microbiota.},
}

@article {pmid39265811,
year = {2024},
author = {Nataraj, BH and Ranveer, SA and K, J and Nagpal, R and Behare, PV},
title = {Immune and Microbiome Modulatory Effects of Limosilactobacillus fermentum NCDC 400 in an Immunocompromised Mouse Model.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106927},
doi = {10.1016/j.micpath.2024.106927},
pmid = {39265811},
issn = {1096-1208},
abstract = {The present study was aimed to assess and validate the safety and functional efficacy of an indigenous probiotic strain Limosilactobacillus fermentum NCDC 400 (hereafter, LFN400) in an immunocompromised murine model. The study included four groups A normal control (NC) group without immune suppression; an experimental model control (MC) with immune suppression induced via intraperitoneal cyclophosphamide (Cy) administration; and two MC groups orally administered with either low dose (LD) or high dose (HD) of LFN400 at dose 10[8] and 10[10] CFU/mouse/day, respectively, for 15-days. Both control groups received normal saline as placebo control. LFN400 improved specific experimental characteristics including hematological and serum biochemical markers. Compared to MC group, LFN400-fed groups showed markedly (P < 0.05) decreased arrays of detrimental cecal enzymes. We did not observe instances of bacterial translocation of LFN400 from gut to bloodstream or extra-intestinal organs. LFN400 intake significantly (P < 0.05) enhanced spleen cell differentiation, immune and oxidative stress markers, and restored Cy-induced histopathological changes in multiple tissues, including the spleen. There was no genotoxic effect of LFN400 on bone marrow cells. Although not statistically significant, LFN400 feeding moderately increased gut microbiome diversity, supporting the growth of beneficial saccharolytic microorganisms and reducing the presence of pathobionts. The findings demonstrate that the probiotic strain LFN400 possesses in vivo safety and immunomodulatory potency and thus should be considered a potential candidate for future human clinical studies.},
}

@article {pmid39265779,
year = {2024},
author = {Xiao, X and Wu, Y and Jie, Z and Lin, L and Li, Y and Hu, W and Li, Y and Zhong, S},
title = {Akkermansia Muciniphila supplementation improving hyperlipidemia, cardiac function, and gut microbiota in high fat fed apolipoprotein E-deficient mice.},
journal = {Prostaglandins & other lipid mediators},
volume = {},
number = {},
pages = {106906},
doi = {10.1016/j.prostaglandins.2024.106906},
pmid = {39265779},
issn = {1098-8823},
abstract = {Hyperlipidemia, obesity and gut dysbiosis are pivotal risk factors for atherosclerotic cardiovascular disease (ACVD). Supplementation of Akkermansia muciniphila (AKK) has also been proven to be effective in the prevention and treatment of obesity and other metabolic disorders. Here we found that AKK was more abundant in healthy control than ACVD patients via metagenomic sequencing on fecal samples. Subsequently, we investigated the role and underlying mechanism of AKK on obesity-associated atherosclerosis. AKK intervention partially reversed the exacerbation of atherosclerotic lesion formation in ApoE[-/-] mice by improving dyslipidemia. Interestingly, replenishment with AKK significantly enhanced cardiac function and reduced the body weight. It also reduced pro-inflammatiory cytokine IL-6 and increased anti-inflammatory IL-10 in the circulation. Additionally, AKK colonization dramatically regulated gut microbiota and increased the abundance of Lactobacillaceae. Our findings have provided novel insights into the therapeutic potential of AKK as a beneficial microbe for treating atherosclerotic-associated cardiovascular diseases.},
}

@article {pmid39264803,
year = {2024},
author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L},
title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387402},
doi = {10.1080/19490976.2024.2387402},
pmid = {39264803},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation & purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; },
abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diterpenes/metabolism/pharmacology
*Biological Availability
Mice
Cholestasis/metabolism/drug therapy/microbiology
Male
RNA, Ribosomal, 16S/genetics
Bile Acids and Salts/metabolism
Bacteria/metabolism/classification/genetics/drug effects/isolation & purification
Humans
Mice, Inbred C57BL
Liver/metabolism/drug effects
Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Disease Models, Animal

@article {pmid39264585,
year = {2024},
author = {Lou, H and Wang, X and Jiang, Q and Li, X and Yao, Y and Chen, Q and Chen, L and Zhang, S and Yu, Y and Liu, C and Zhou, H},
title = {Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/23744235.2024.2402921},
pmid = {39264585},
issn = {2374-4243},
abstract = {OBJECTIVE: Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a.

METHODS: We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology.

RESULTS: The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%).

CONCLUSIONS: Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.},
}

@article {pmid39264513,
year = {2024},
author = {Angebault, C and Botterel, F},
title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.},
journal = {Mycopathologia},
volume = {189},
number = {5},
pages = {82},
pmid = {39264513},
issn = {1573-0832},
mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Microbiota ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.},
}

*Cystic Fibrosis/microbiology/complications
Humans
*Mycobiome
*Metagenomics/methods
Fungi/genetics/classification/isolation & purification
Respiratory System/microbiology
Bacteria/genetics/classification/isolation & purification
Lung/microbiology
Microbiota

@article {pmid39264158,
year = {2024},
author = {Wang, X and Guo, X and Liu, H and Wang, B and Wu, J and Chen, S and Zhang, W and Zhang, X and Wang, X},
title = {Augmented pathogen detection in brain abscess using metagenomic next-generation sequencing: a retrospective cohort study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0032524},
doi = {10.1128/spectrum.00325-24},
pmid = {39264158},
issn = {2165-0497},
abstract = {Brain abscess is a severe infection characterized by the accumulation of pus within the brain parenchyma. Accurate identification of the causative pathogens is crucial for effective treatment and improved patient outcomes. This 10-year retrospective, single-center study aimed to compare the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) in brain abscess. We reviewed 612 patients diagnosed with brain abscess and identified 174 cases with confirmed etiology. The median age was 52 years, with 69.5% males. Culture tests predominately identified gram-positive bacteria, particularly Streptococcus spp. Gram-negative bacteria, including Klebsiella spp., were also detected. However, mNGS revealed a more diverse pathogen spectrum, focusing on anaerobes (e.g., Fusobacterium spp., Parvimonas spp., Porphyromonas spp., Prevotella spp., and Tannerella spp.). mNGS exhibited significantly higher overall pathogen-positive rates in pus samples (85.0% vs 50.0%, P = 0.0181) and CSF samples (84.2% vs 7.9%, P < 0.0001) compared to culture. Furthermore, the detection rates for anaerobes displayed a notable disparity, with mNGS yielding significantly higher positive detections in both pus samples (50.0% vs 10%, P = 0.0058) and CSF samples (18.4% vs 0%, P = 0.0115) when compared to culture methods. The assistance of mNGS in pathogen detection, particularly anaerobes in brain abscess, was evident in our findings. mNGS demonstrated the ability to identify rare and fastidious pathogens, even in culture-negative cases. These results emphasize the clinical value of mNGS as a supplement for brain abscess, enabling more comprehensive and accurate pathogen identification.IMPORTANCEThe accurate identification of pathogens causing brain abscess is crucial for effective treatment and improved patient outcomes. In this 10-year retrospective study, the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) was compared. The study analyzed 612 patients with brain abscess and confirmed etiology in 174 cases. The results showed that culture tests predominantly identified gram-positive bacteria, while mNGS unveiled a broader diverse pathogen spectrum, particularly anaerobes. The mNGS method exhibited significantly higher overall rates of pathogen positivity both in pus and cerebrospinal fluid (CSF) samples, surpassing the culture methods. Notably, mNGS detected a significantly higher number of anaerobes in both pus and CSF samples compared to culture methods. These findings underscore the clinical value of mNGS as a supplement for brain abscess diagnosis, enabling more comprehensive and accurate pathogen identification, particularly for rare and fastidious pathogens that evade detection by conventional culture methods.},
}

@article {pmid39264053,
year = {2024},
author = {Ho, L and Lai, C and Daim, LDJ and Noh, NM and Yap, Y and Ibrahim, J and Teh, C},
title = {Deciphering Root-associated Microbial Communities in Asymptomatic Oil Palm Seedlings Exposed to Ganoderma boninense: New Insight into Disease Tolerance of Oil Palms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae122},
pmid = {39264053},
issn = {1574-6941},
abstract = {Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.},
}

@article {pmid39263696,
year = {2024},
author = {Nag, M and Pallavi, J and Chakraborty, S and Roychoudhury, T and Mondal, S and Ghosh, A and Saha, C and Banerjee, M and Seal, A},
title = {Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 - insights into a yet unknown micro-ecosystem.},
journal = {Molecular omics},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3mo00273j},
pmid = {39263696},
issn = {2515-4184},
abstract = {Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.},
}

@article {pmid39263550,
year = {2024},
author = {Bell, E and Chen, J and Richardson, WDL and Fustic, M and Hubert, CRJ},
title = {Denitrification genotypes of endospore-forming Bacillota.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae107},
doi = {10.1093/ismeco/ycae107},
pmid = {39263550},
issn = {2730-6151},
abstract = {Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.},
}

@article {pmid39263297,
year = {2024},
author = {Wang, A and Cui, X and Shi, C},
title = {Metagenomic analysis of rats with diarrhea treated with mixed probiotics: response to consecutive and alternate-hour supplementation.},
journal = {Translational pediatrics},
volume = {13},
number = {8},
pages = {1336-1358},
doi = {10.21037/tp-24-129},
pmid = {39263297},
issn = {2224-4344},
abstract = {BACKGROUND: Diarrhea is the leading contributory factor of sickness and mortality among children under five and an economic burden for families. This study aimed to investigate the effects of mixed probiotics supplementation at different times (consecutive and alternate-hour) on intestinal microecology in Sprague-Dawley (SD) rats with acute diarrhea.

METHODS: A total of 40 SD rats were randomly assigned to four groups, including the control group, model group, probiotic group A, and probiotic group B. An acute diarrhea model was induced by administration of 5% dextran sulfate sodium. Rats in probiotic group A and probiotic group B were fed with Clostridium butyricum (C. butyricum), Bifidobacterium infantis (B. infantis), and Saccharomyces boulardii (S. boulardii) for a total of 7 days. Probiotic group A was fed with all probiotics simultaneously. Probiotic group B was fed with C. butyricum and B. infantis simultaneously, and then after a 2-hour interval, with S. boulardii. Metagenomic next-generation sequencing was used to analyze the fecal samples from every rat. The metagenomic sequencing used in this experiment was used to evaluate the effect of probiotics on the composition as well as function of the gut microbiota in order to gain a deeper comprehension of probiotic-host interactions on health and disease.

RESULTS: The structure of the gut microbiota in probiotic group A showed significant changes. Compared to the model group, the abundance of some beneficial bacteria had increased, including Actinobacteria (P=0.048), Lactobacillus (P=0.050), and Lactobacillus johnsonii (P=0.042), and many opportunistic pathogenic bacteria has decreased, such as Ruminococcus (P=0.001). Compared to the control group, the abundance of some beneficial bacteria had increased, including Fusobacteria (P=0.02) and Phascolarium (P=0.002), and there was a reduction in the abundance of many opportunistic pathogenic bacteria such as Roseburia (P=0.03), Lachnoclosterium (P=0.009), and Oscillibacter_sp_1-3 (P=0.002). In addition, metagenomic analysis showed that as well as an up-regulation of glycoside hydrolase expression, amino acid and inorganic ion transport, and metabolism-related pathways, there was a down-regulation of cell motility.

CONCLUSIONS: Simultaneous administration of probiotics may have more positive implications in improving the gut microbiota of acute diarrhea rats.},
}

@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
doi = {10.12688/f1000research.134798.2},
pmid = {39262445},
issn = {2046-1402},
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}

*Metagenomics/methods
Humans
*Metadata
High-Throughput Nucleotide Sequencing/methods
Software
Metagenome
Computational Biology/methods
DNA, Ancient/analysis

@article {pmid39262440,
year = {2024},
author = {Hallgren, MB and Clausen, PTLC and Aarestrup, FM},
title = {NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.},
journal = {Biology methods & protocols},
volume = {9},
number = {1},
pages = {bpae057},
doi = {10.1093/biomethods/bpae057},
pmid = {39262440},
issn = {2396-8923},
abstract = {Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variants, thereby achieving a good balance between sensitivity and precision. A comparative evaluation of NanoMGT, using a simulated multi-strain sample of seven bacterial species, demonstrated superior performance relative to existing tools and the advantages of using a threshold-based filtering approach to calling minority variants in ONT's sequencing data. NanoMGT's potential as a post-binning tool in metagenomic pipelines is particularly notable, enabling researchers to more accurately determine specific alleles and understand strain diversity in microbial communities. Our findings have significant implications for clinical diagnostics, environmental microbiology, and the broader field of genomics. The findings offer a reliable and efficient approach to marker gene typing in complex metagenomic samples.},
}

@article {pmid39261970,
year = {2024},
author = {Wan, X and Shahrear, S and Chew, SW and Vilaplana, F and Mäkelä, MR},
title = {Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {17},
number = {1},
pages = {120},
pmid = {39261970},
issn = {2731-3654},
support = {NNF21OC0071410//Novo Nordisk Fonden/ ; HiLIFE Fellows grant 2023-2025//Helsinki Institute of Life Science, Helsingin Yliopisto/ ; },
abstract = {BACKGROUND: Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods.

RESULTS: This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method.

CONCLUSIONS: This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.},
}

@article {pmid39261503,
year = {2024},
author = {Schwab, S and Hu, Y and van Erp, B and Cajili, MKM and Hartmann, MD and Hernandez Alvarez, B and Alva, V and Boyle, AL and Dame, RT},
title = {Histones and histone variant families in prokaryotes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7950},
pmid = {39261503},
issn = {2041-1723},
support = {OCENW.GROOT.2019.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {*Histones/metabolism/chemistry/genetics ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; Prokaryotic Cells/metabolism ; Phylogeny ; Nucleosomes/metabolism ; Models, Molecular ; Archaeal Proteins/metabolism/chemistry/genetics ; Amino Acid Sequence ; },
abstract = {Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.},
}

*Histones/metabolism/chemistry/genetics
*Archaea/metabolism/genetics
*Bacteria/metabolism/genetics
Prokaryotic Cells/metabolism
Phylogeny
Nucleosomes/metabolism
Models, Molecular
Archaeal Proteins/metabolism/chemistry/genetics
Amino Acid Sequence

@article {pmid39260724,
year = {2024},
author = {Ke, Y and Sun, W and Xue, Y and Yuan, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S},
title = {Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119964},
doi = {10.1016/j.envres.2024.119964},
pmid = {39260724},
issn = {1096-0953},
abstract = {Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms' activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.},
}

@article {pmid39260513,
year = {2024},
author = {Tan, J and Wang, Y and Niu, H and Li, L and Zhao, H and Fang, L and Jiang, L and Zhao, Y and Zhao, Y},
title = {Metagenomic insights into the mechanistic differences of plant polyphenols and nitrocompounds in reducing methane emissions using the rumen simulation technique.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176135},
doi = {10.1016/j.scitotenv.2024.176135},
pmid = {39260513},
issn = {1879-1026},
abstract = {Methane (CH4) emissions from ruminants contribute significantly to greenhouse gas levels and also result in considerable feed energy losses. Plant polyphenols and nitrocompounds are two typical types of methane inhibitors. The study investigates the mechanistic differences between 2-nitroethanol (NE) and proanthocyanidins (PAC) in reducing methane emissions from ruminant livestock using the rumen simulation technique (RUSITEC) combined with metagenomic analyses. The experiment was performed as a complete randomized block design with 3 runs. Run was used as a blocking factor. The treatments included a control (CON) with no additive, NE at 0.5 g/kg dry matter (DM), and PAC at 20 g/kg DM, all incubated in vitro for 24 h (h) with eight replicates per treatment. The results showed that NE significantly reduced CH4 production by 94.9 % (P < 0.01) and total volatile fatty acid (TVFA) concentration by 11.1 % (P < 0.05) compared to the control. NE also decreased the acetate-to-propionate ratio (A/P) from 1.93 to 1.60 (P < 0.01), indicating a shift towards more efficient fermentation. In contrast, PAC reduced methane production by 11.7 % (P < 0.05) and decreased the A/P (P < 0.05) while maintaining microbial diversity and fermentation stability, with no significant impact on TVFA concentration (P > 0.05). Metagenomic analysis revealed that NE markedly suppressed the abundance of key genera involved in carbohydrate metabolism, including Prevotella and Bacteroides, leading to reduced acetate and butyrate pathways. NE also selectively inhibited methanogenic archaea, particularly Methanobrevibacter spp., which are integral to the hydrogenotrophic pathway (P < 0.01). On the other hand, PAC showed selective inhibition of Methanosphaera spp., targeting the methylotrophic pathway (P < 0.01). These findings provide valuable insights into the distinct microbial and metabolic pathways modulated by NE and PAC, offering potential strategies for developing effective dietary interventions to mitigate methane emissions in ruminant livestock.},
}

@article {pmid39260494,
year = {2024},
author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S},
title = {Metagenomic approaches and opportunities in arid soil research.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176173},
doi = {10.1016/j.scitotenv.2024.176173},
pmid = {39260494},
issn = {1879-1026},
abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.},
}

@article {pmid39260483,
year = {2024},
author = {Li, W and Wang, H and Lv, G and Wang, J and Li, J},
title = {Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176148},
doi = {10.1016/j.scitotenv.2024.176148},
pmid = {39260483},
issn = {1879-1026},
abstract = {Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.},
}

@article {pmid39260018,
year = {2024},
author = {Chen, M and Chen, Y and He, X and Hao, R and Jiang, X and Ji, Y and Zhuo, B and Xu, W and Lin, R and Ge, Y},
title = {A case of Bartonella vinsonii endocarditis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {4},
pages = {116535},
doi = {10.1016/j.diagmicrobio.2024.116535},
pmid = {39260018},
issn = {1879-0070},
abstract = {The diagnosis of Bartonella is challenging due to its rarity and negative culture results. Once the diagnosis is delayed and proper treatment is not given, it can develop into infective endocarditis, which can be fatal. We reported a 60-year-old female patient who had recurrent fever for 5 months. After receiving ineffective treatment at the local hospital, she sought medical attention at our hospital. Laboratory blood indicators testing and imaging indicated infective endocarditis, and metagenomic Next Generation Sequencing (m-NGS) testing confirmed the diagnosis of Bartonella vinsonii infection. After surgical treatment and the combination of doxycycline and ceftriaxone sodium for anti-infective therapy, the patient recovered. Valuing the combination of multiple auxiliary diagnostic methods and improving the application of m-NGS in the detection of unknown pathogens can compensate for the current limitations in the diagnosis of Bartonella. Early diagnosis and treatment are extremely important for Bartonella endocarditis.},
}

@article {pmid39259188,
year = {2024},
author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A},
title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae169},
pmid = {39259188},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestAntibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.},
}

@article {pmid39258944,
year = {2024},
author = {Zhu, W and Zeng, Z and Xia, J and Li, L},
title = {Achieving rapid start-up and efficient nitrogen removal of partial-denitrification/anammox process using organic matter in brewery wastewater as carbon source.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/09593330.2024.2401157},
pmid = {39258944},
issn = {1479-487X},
abstract = {To find a cost-efficient carbon source for the partial denitrification/anaerobic ammonium oxidation (anammox) (PD/A) process, the practicability of using the organic matter contained in brewery wastewater as carbon source was investigated. Quick self-enrichment of denitrifying bacteria was achieved by supplying brewery wastewater as organic carbon source and using the mature anammox sludge as the seeding sludge. The PD/A process was successfully established after 33-day operation and then the average total nitrogen removal efficiency reached 92.29% when the influent CODCr: NO3[-]-N: NH4[+]-N ratio was around 2.5: 1.0: 0.67. The relative abundance of Thauera increased from 0.03% in the seeding sludge to 54.29% on day 110, whereas Candidatus brocadia decreased from 30.66% to 2.08%. The metagenomic analysis indicated that the sludge on day 110 contained more nar and napA (total of 41.24%) than nirK and nirS (total of 11.93%). Thus NO2[-]-N was accumulated efficiently in the process of denitrification and sufficient NO2[-]-N was supplied for anammox bacteria in the PD/A process. Using brewery wastewater as carbon source not only saved the cost of nitrogen removal but also converted waste into resource and reduced the treatment expense of brewery wastewater.},
}

@article {pmid39258715,
year = {2024},
author = {Vats, R and Yadav, P and Bano, A and Wadhwa, S and Bhardwaj, R},
title = {Salivary biomarkers in non-invasive oral cancer diagnostics: a comprehensive review.},
journal = {Journal of applied oral science : revista FOB},
volume = {32},
number = {},
pages = {e20240151},
doi = {10.1590/1678-7757-2024-0151},
pmid = {39258715},
issn = {1678-7765},
mesh = {Humans ; *Mouth Neoplasms/diagnosis ; *Saliva/chemistry/virology ; *Biomarkers, Tumor/analysis ; Early Detection of Cancer/methods ; },
abstract = {OBJECTIVE: This review aims to provide a comprehensive analysis of the effectiveness of saliva as a non-invasive diagnostic marker for oral cancer. Despite progress in oral cancer diagnosis and prognosis, the 5-year survival rate remains low due to the resistance to treatment and delayed diagnosis, which can be attributed to various factors including tobacco and alcohol consumption, genetic damage, and human papillomavirus (HPV). The potential use of saliva as an easily accessible non-invasive screening and diagnostic method arises from its direct contact with the lesion site.

METHODOLOGY: Data for this study were gathered via a comprehensive literature evaluation using search engines such as the PubMed, Web of Science, Google Scholar, and SciFinder.

RESULTS: Identifying salivary biomarkers shows potential to transform oral cancer diagnostics by offering a reliable alternative to the traditional invasive methods. Saliva is an abundant reservoir for both cell-bound and cell-free organic and inorganic constituents. Thus, saliva is an appropriate field for research in proteomics, genomics, metagenomics, and metabolomics.

CONCLUSION: This review provides a comprehensive elucidation of salivary biomarkers and their function in non-invasive oral cancer diagnosis, demonstrating their potential to enhance patient outcomes and reduce the impact of this devastating disease.},
}

Humans
*Mouth Neoplasms/diagnosis
*Saliva/chemistry/virology
*Biomarkers, Tumor/analysis
Early Detection of Cancer/methods

@article {pmid39258254,
year = {2024},
author = {Sun, W and Zheng, L and Kang, L and Chen, C and Wang, L and Lu, L and Wang, F},
title = {Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1451440},
doi = {10.3389/fcimb.2024.1451440},
pmid = {39258254},
issn = {2235-2988},
mesh = {*Bronchoalveolar Lavage Fluid/microbiology/virology ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Multiplex Polymerase Chain Reaction/methods ; Aged ; Bacteria/isolation & purification/genetics/classification ; Respiratory Tract Infections/diagnosis/virology/microbiology ; Viruses/isolation & purification/genetics/classification ; Molecular Diagnostic Techniques/methods ; Young Adult ; },
abstract = {BACKGROUND: Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens.

METHODS: In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR.

RESULTS: The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including Human gammaherpesvirus 4 (P<0.001), Human betaherpesvirus 7 (P<0.001), Human betaherpesvirus 5 (P<0.05) and Human betaherpesvirus 6 (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR.

CONCLUSIONS: Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.},
}

*Bronchoalveolar Lavage Fluid/microbiology/virology
Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Male
Middle Aged
Adult
Multiplex Polymerase Chain Reaction/methods
Aged
Bacteria/isolation & purification/genetics/classification
Respiratory Tract Infections/diagnosis/virology/microbiology
Viruses/isolation & purification/genetics/classification
Molecular Diagnostic Techniques/methods
Young Adult

@article {pmid39257939,
year = {2024},
author = {Markam, SS and Raj, A and Kumar, A and Khan, ML},
title = {Microbial biosurfactants: Green alternatives and sustainable solution for augmenting pesticide remediation and management of organic waste.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100266},
doi = {10.1016/j.crmicr.2024.100266},
pmid = {39257939},
issn = {2666-5174},
abstract = {Pesticide pollution remains a significant environmental challenge, necessitating the exploration of sustainable alternatives. Biosurfactants are a class of unconventional surface-active chemicals that are produced by microorganisms. Biosurfactants have many applications in treating oil spills, emulsifiers, pharmaceuticals, and agriculture. Compared to chemical surfactants, they have benefits such as biodegradability, less toxicity, and a greener option because they are derived from microbes. Biosurfactants have recently been shown to have the potential to speed up pesticide cleanup. Biosurfactants are used in pesticide remediation because of their exceptional foaming ability, high selectivity, and wide range of pH, salinity, and temperature operating windows. Microbial biosurfactants emerged as potential agents for the treatment of organic waste and agricultural residue. This review unfolds the promising realm of microbial biosurfactants as green solutions for environmental sustainability, particularly in agricultural practices, with special reference to pesticide remediation. This article highlights the escalating need for eco-friendly alternatives, paving the way for discussing biosurfactants. Moreover, the articles discuss in detail various advancements in the field of rapid screening of biosurfactants, either using a conventional approach or via advanced instruments such as GC-MS, HPLC, NMR, FTIR, etc. Furthermore, the article unveils the molecular mechanisms and the microbial genes driving biosurfactant synthesis, offering insights into enhancing production efficiency. Moreover, the article explores diverse applications of microbial biosurfactants in sustainable agriculture, ranging from soil remediation to crop protection. The article also highlights the various functions of microbial biosurfactants for enhancing the decomposition and recycling of organic waste and agricultural residues, emphasizing their potential for sustainable waste management strategies. Overall, the review underscores the pivotal role of microbial biosurfactants as green alternatives for addressing pesticide pollution and advancing environmental sustainability.},
}

@article {pmid39257028,
year = {2024},
author = {Jotta, VFM and García, GJY and Fonseca, PLC and de Mello Ferreira, A and Azevedo, V and Brenig, B and Góes-Neto, A and Badotti, F},
title = {Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae231},
pmid = {39257028},
issn = {1365-2672},
abstract = {AIMS: Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation.

METHODS AND RESULTS: In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2 030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed more than 12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria.

CONCLUSIONS: Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.},
}

@article {pmid39256724,
year = {2024},
author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN},
title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {1124},
pmid = {39256724},
issn = {1471-2407},
support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; *Feces/microbiology ; Female ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Asian People ; Colon/microbiology ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.

METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n = 112) and colonic tissue (n = 36) in 112 individuals. The cohort comprised of individuals with CRC (n = 24), premalignant lesions (n = 10), healthy individuals (n = 50) and in those with diabetes (n = 28).

RESULTS: Overall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p < 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.

CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.},
}

Humans
*Colorectal Neoplasms/microbiology
Male
*Feces/microbiology
Female
Middle Aged
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Aged
RNA, Ribosomal, 16S/genetics
Adult
Asian People
Colon/microbiology
Bacteria/genetics/classification/isolation & purification
Metagenome

@article {pmid39256682,
year = {2024},
author = {Wu, LH and Hu, CX and Liu, TX},
title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {337},
pmid = {39256682},
issn = {1471-2180},
mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.

METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.

RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-β-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.

CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.},
}

Animals
*Spodoptera/microbiology/genetics
*Larva/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics
*Zea mays/microbiology
*Bacteria/classification/genetics/isolation & purification
*Sorghum/microbiology
Solanum lycopersicum/microbiology
Capsicum/microbiology
Metagenome

@article {pmid39256599,
year = {2024},
author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP},
title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21168},
pmid = {39256599},
issn = {2045-2322},
support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; },
abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.},
}

*Ginsenosides/pharmacokinetics/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
Rats
Male
*Bacteroides/drug effects
Rats, Sprague-Dawley
Glycoside Hydrolases/metabolism

@article {pmid39256479,
year = {2024},
author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M},
title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {989},
pmid = {39256479},
issn = {2052-4463},
mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; },
abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.},
}

*Ecosystem
Plankton
Metagenome
Biodiversity
Metagenomics

@article {pmid39256206,
year = {2024},
author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO},
title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {918},
pmid = {39256206},
issn = {1573-2959},
mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; },
abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.},
}

Nigeria
*Geologic Sediments/microbiology/chemistry
*Environmental Monitoring
*Microbiota
*Water Pollutants, Chemical/analysis
Metals, Heavy/analysis
Anthropogenic Effects
Bacteria/classification/genetics
Hydrocarbons/analysis

@article {pmid39255933,
year = {2024},
author = {Kim, Y and Choe, S and Cho, Y and Moon, H and Shin, H and Seo, J and Myung, J},
title = {Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176129},
doi = {10.1016/j.scitotenv.2024.176129},
pmid = {39255933},
issn = {1879-1026},
abstract = {Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradability of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed via biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradability regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.},
}

@article {pmid39255566,
year = {2024},
author = {Quan, H and Jia, Y and Zhang, H and Ji, F and Shi, Y and Deng, Q and Hao, T and Khanal, SK and Sun, L and Lu, H},
title = {Insights into the role of electrochemical stimulation on sulfur-driven biodegradation of antibiotics in wastewater treatment.},
journal = {Water research},
volume = {266},
number = {},
pages = {122385},
doi = {10.1016/j.watres.2024.122385},
pmid = {39255566},
issn = {1879-2448},
abstract = {The presence of antibiotics in wastewater poses significant threat to our ecosystems and health. Traditional biological wastewater treatment technologies have several limitations in treating antibiotic-contaminated wastewaters, such as low removal efficiency and poor process resilience. Here, a novel electrochemical-coupled sulfur-mediated biological system was developed for treating wastewater co-contaminated with several antibiotics (e.g., ciprofloxacin (CIP), sulfamethoxazole (SMX), chloramphenicol (CAP)). Superior removal of CIP, SMX, and CAP with efficiencies ranging from 40.6 ± 2.6 % to 98.4 ± 1.6 % was achieved at high concentrations of 1000 μg/L in the electrochemical-coupled sulfur-mediated biological system, whereas the efficiencies ranged from 30.4 ± 2.3 % to 98.2 ± 1.4 % in the control system (without electrochemical stimulation). The biodegradation rates of CIP, SMX, and CAP increased by 1.5∼1.9-folds under electrochemical stimulation compared to the control. The insights into the role of electrochemical stimulation for multiple antibiotics biodegradation enhancement was elucidated through a combination of metagenomic and electrochemical analyses. Results showed that sustained electrochemical stimulation significantly enriched the sulfate-reducing and electroactive bacteria (e.g., Desulfobulbus, Longilinea, and Lentimicrobiumin on biocathode and Geobactor on bioanode), and boosted the secretion of electron transport mediators (e.g., cytochrome c and extracellular polymeric substances), which facilitated the microbial extracellular electron transfer processes and subsequent antibiotics removal in the sulfur-mediated biological system. Furthermore, under electrochemical stimulation, functional genes associated with sulfur and carbon metabolism and electron transfer were more abundant, and the microbial metabolic processes were enhanced, contributing to antibiotics biodegradation. Our study for the first time demonstrated that the synergistic effects of electrochemical-coupled sulfur-mediated biological system was capable of overcoming the limitations of conventional biological treatment processes. This study shed light on the mechanism of enhanced antibiotics biodegradation via electrochemical stimulation, which could be employed in sulfur-mediated bioprocess for treating antibiotic-contaminated wastewaters.},
}

@article {pmid39255397,
year = {2024},
author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R},
title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S95-S108},
doi = {10.1093/infdis/jiae165},
pmid = {39255397},
issn = {1537-6613},
support = {//Infectious Diseases Society of America/ ; //Foundation/ ; 23A02//Florida Department of Health/ ; 440658//US Department of Agriculture/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; R01 AG070094/NH/NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.

METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.

RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.

CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.},
}

Animals
Mice
*Mice, Transgenic
*Klebsiella pneumoniae
*Disease Models, Animal
*Dysbiosis/microbiology/chemically induced
*Alzheimer Disease/microbiology
*Neuroinflammatory Diseases/microbiology
*Gastrointestinal Microbiome/drug effects
*Klebsiella Infections/microbiology
*Blood-Brain Barrier/microbiology
Brain/pathology/microbiology
Anti-Bacterial Agents/pharmacology
Brain-Gut Axis
Male
Humans

@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 = {},
number = {},
pages = {e0030124},
doi = {10.1128/msystems.00301-24},
pmid = {39254351},
issn = {2379-5077},
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.},
}

@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 = {},
number = {},
pages = {e0036224},
doi = {10.1128/msystems.00362-24},
pmid = {39254336},
issn = {2379-5077},
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.},
}

@article {pmid39254265,
year = {2024},
author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N},
title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2398126},
doi = {10.1080/19490976.2024.2398126},
pmid = {39254265},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; },
abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Mice, Inbred C57BL
*Bacteria/classification/genetics/isolation & purification/immunology
Intestines/microbiology/immunology/cytology
Metagenomics
Germ-Free Life
Female
T-Lymphocyte Subsets/immunology
Male
Intestinal Mucosa/microbiology/immunology/cytology

@article {pmid39254230,
year = {2024},
author = {Qi, Q and Ning, S and Guo, X and Zhao, J and Tian, R and Gui, H and He, JS and Wang, H and Zhang, Z and Konstantinidis, KT and Gao, Q and Wang, Y and Li, S and Zhao, W and Yang, Y and Zhou, J},
title = {More sensitive microbial responses to the interactive effects of warming and altered precipitation in subsoil than topsoil of an alpine grassland ecosystem.},
journal = {Global change biology},
volume = {30},
number = {9},
pages = {e17487},
doi = {10.1111/gcb.17487},
pmid = {39254230},
issn = {1365-2486},
support = {//the CAS Youth Interdisciplinary Team/ ; 32161123002//National Natural Science Foundation of China/ ; 42277213//National Natural Science Foundation of China/ ; 41907209//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 32130065//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Soil Microbiology ; *Grassland ; *Climate Change ; *Rain ; *Carbon Cycle ; *Soil/chemistry ; Tibet ; Carbon/analysis/metabolism ; Global Warming ; Bacteria/genetics/classification ; },
abstract = {Subsoil is a large organic carbon reservoir, storing more than half of the total soil organic carbon (SOC) globally. Conventionally, subsoil is assumed to not be susceptible to climate change, but recent studies document that climate change could significantly alter subsoil carbon cycling. However, little is known about subsoil microbial responses to the interactive effects of climate warming and altered precipitation. Here, we investigated carbon cycling and associated microbial responses in both subsoil (30-40 cm) and topsoil (0-10 cm) in a Tibetan alpine grassland over 4 years of warming and altered precipitation. Compared to the unchanged topsoil carbon (β = .55, p = .587), subsoil carbon exhibited a stronger response to the interactive effect of warming and altered precipitation (β = 2.04, p = .021), that is, warming decreased subsoil carbon content by 28.20% under decreased precipitation while warming increased subsoil carbon content by 18.02% under increased precipitation.Furthermore, 512 metagenome-assembled genomes (MAGs) were recovered, including representatives of phyla with poor genomic representation. Compared to only one changed topsoil MAG, 16 subsoil MAGs were significantly affected by altered precipitation, and 5 subsoil MAGs were significantly affected by the interactive effect of warming and precipitation. More than twice as many populations whose MAG abundances correlated significantly with the variations of carbon content, components and fluxes were observed in the subsoil than topsoil, suggesting their potential contribution in mediating subsoil carbon cycling. Collectively, our findings highlight the more sensitive responses of specific microbial lineages to the interactive effects of warming and altered precipitation in the subsoil than topsoil, and provide key information for predicting subsoil carbon cycling under future climate change scenarios.},
}

*Soil Microbiology
*Grassland
*Climate Change
*Rain
*Carbon Cycle
*Soil/chemistry
Tibet
Carbon/analysis/metabolism
Global Warming
Bacteria/genetics/classification

@article {pmid39254049,
year = {2024},
author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI},
title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0055724},
doi = {10.1128/msphere.00557-24},
pmid = {39254049},
issn = {2379-5042},
abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.},
}

@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 = {},
number = {},
pages = {e14226},
doi = {10.1111/apha.14226},
pmid = {39253815},
issn = {1748-1716},
support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsches Zentrum für Herz-Kreislaufforschung/ ; },
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.},
}

@article {pmid39253787,
year = {2024},
author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M},
title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20118},
pmid = {39253787},
issn = {1469-8137},
support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&D program/ ; },
abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.},
}

@article {pmid39253606,
year = {2024},
author = {Qin, Y and Zou, X and Jin, Y and Li, J and Cai, Q},
title = {Cryptococcus Neoformans Osteomyelitis of the Right Ankle Diagnosed by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient with Tuberculous Lymphadenitis and Pulmonary Tuberculosis: A Case Report and Recent Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3805-3812},
doi = {10.2147/IDR.S476270},
pmid = {39253606},
issn = {1178-6973},
abstract = {AIM: Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios.

CASE PRESENTATION: We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms.

CONCLUSION: Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections.},
}

@article {pmid39253579,
year = {2024},
author = {Wang, X and Yang, J and Ren, B and Yang, G and Liu, X and Xiao, R and Ren, J and Zhou, F and You, L and Zhao, Y},
title = {Comprehensive multi-omics profiling identifies novel molecular subtypes of pancreatic ductal adenocarcinoma.},
journal = {Genes & diseases},
volume = {11},
number = {6},
pages = {101143},
doi = {10.1016/j.gendis.2023.101143},
pmid = {39253579},
issn = {2352-3042},
abstract = {Pancreatic cancer, a highly fatal malignancy, is predicted to rank as the second leading cause of cancer-related death in the next decade. This highlights the urgent need for new insights into personalized diagnosis and treatment. Although molecular subtypes of pancreatic cancer were well established in genomics and transcriptomics, few known molecular classifications are translated to guide clinical strategies and require a paradigm shift. Notably, chronically developing and continuously improving high-throughput technologies and systems serve as an important driving force to further portray the molecular landscape of pancreatic cancer in terms of epigenomics, proteomics, metabonomics, and metagenomics. Therefore, a more comprehensive understanding of molecular classifications at multiple levels using an integrated multi-omics approach holds great promise to exploit more potential therapeutic options. In this review, we recapitulated the molecular spectrum from different omics levels, discussed various subtypes on multi-omics means to move one step forward towards bench-to-beside translation of pancreatic cancer with clinical impact, and proposed some methodological and scientific challenges in store.},
}

@article {pmid39253412,
year = {2024},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DD and Wells, DM and Moreno, Â and Castrillo, G and Wagner, MR},
title = {Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.26.609769},
pmid = {39253412},
issn = {2692-8205},
abstract = {Both chronic and acute drought alter the composition and physiology of soil microbiomes, with implications for globally important processes including carbon cycling and plant productivity. When water is scarce, selection favors microbes with thicker peptidoglycan cell walls, sporulation ability, and constitutive osmolyte production (Schimel, Balser, and Wallenstein 2007)-but also the ability to degrade complex plant-derived polysaccharides, suggesting that the success of plants and microbes during drought are inextricably linked. However, communities vary enormously in their drought responses and subsequent interactions with plants. Hypothesized causes of this variation in drought resilience include soil texture, soil chemistry, and historical precipitation patterns that shaped the starting communities and their constituent species (Evans, Allison, and Hawkes 2022). Currently, the physiological and molecular mechanisms of microbial drought responses and microbe-dependent plant drought responses in diverse natural soils are largely unknown (de Vries et al. 2023). Here, we identify numerous microbial taxa, genes, and functions that characterize soil microbiomes with legacies of chronic water limitation. Soil microbiota from historically dry climates buffered plants from the negative effects of subsequent acute drought, but only for a wild grass species native to the same region, and not for domesticated maize. In particular, microbiota with a legacy of chronic water limitation altered the expression of a small subset of host genes in crown roots, which mediated the effect of acute drought on transpiration and intrinsic water use efficiency. Our results reveal how long-term exposure to water stress alters soil microbial communities at the metagenomic level, and demonstrate the resulting "legacy effects" on neighboring plants in unprecedented molecular and physiological detail.},
}

@article {pmid39253328,
year = {2024},
author = {Gao, Z and Zheng, W and Zhang, M and Gao, Y and Huang, J and Chen, X and Dai, Z and Song, Z and Feng, J and Cao, Q and Jin, Y},
title = {Metagenomic next-generation sequencing promotes pathogen detection over culture in joint infections with previous antibiotic exposure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1388765},
doi = {10.3389/fcimb.2024.1388765},
pmid = {39253328},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; *Synovial Fluid/microbiology ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Sensitivity and Specificity ; Adult ; Arthritis, Infectious/microbiology/diagnosis/drug therapy ; },
abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from joint infection (JI) synovial fluid (SF) samples with previous antibiotic exposure.

METHODS: From January 2019 to January 2022, 59 cases with suspected JI were enrolled. All cases had antibiotic exposure within 2 weeks before sample collection. mNGS and conventional culture were performed on SF samples. JI was diagnosed based on history and clinical symptoms in conjunction with MSIS criteria. The diagnostic values, including sensitivity, specificity, positive/negative predictive values (PPV/NPV), and accuracy, were in comparison with mNGS and culture.

RESULTS: There were 47 of the 59 cases diagnosed with JI, while the remaining 12 were diagnosed with non-infectious diseases. The sensitivity of mNGS was 68.1%, which was significantly higher than that of culture (25.5%, p<0.01). The accuracy of mNGS was significantly higher at 71.2% compared to the culture at 39.0% (p <0.01). Eleven pathogenic strains were detected by mNGS but not by microbiological culture, which included Staphylococcus lugdunensis, Staphylococcus cohnii, Finegoldia magna, Enterococcus faecalis, Staphylococcus saprophytics, Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Acinetobacter pittii, Brucella ovis, andCoxiella burnetii. Antibiotic therapy was adjusted based on the mNGS results in 32 (68.1%) patients, including 12 (25.5%) and 20 (42.6%) patients, in whom treatment was upgraded and changed, respectively. All JI patients underwent surgery and received subsequent antibiotic therapy. They were followed up for an average of 23 months (20-27 months), and the success rate of treatment was 89.4%. Out of the 33 patients who had positive results for pathogens, reoperation was performed in 1 case (3.03%), while out of the 14 cases with negative results for both mNGS and cultures, reoperation was performed in 4 cases (28.6%).

CONCLUSIONS: mNGS has advantages over conventional culture in detecting pathogens in SF samples from JI patients previously treated with antibiotics, potentially improving clinical outcomes.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/therapeutic use/pharmacology
Male
Female
Middle Aged
Aged
*Synovial Fluid/microbiology
*Bacteria/genetics/isolation & purification/classification/drug effects
Sensitivity and Specificity
Adult
Arthritis, Infectious/microbiology/diagnosis/drug therapy

@article {pmid39253237,
year = {2024},
author = {Zhuang, L and Zhu, C and Ma, J and Zhu, D and Zhu, H and Zhong, S and Liu, X and Wang, Z and Yang, Z and Zhang, W and Ding, R and Chen, D and Zheng, S},
title = {Predictive performance of Metagenomic Next Generation Sequencing in early detection of post-liver transplantation infections.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e36405},
doi = {10.1016/j.heliyon.2024.e36405},
pmid = {39253237},
issn = {2405-8440},
abstract = {OBJECTIVE: To evaluate the predictive performance of metagenomic next-generation sequencing (mNGS) in identifying and predicting pulmonary infections following liver transplantation and to investigate its association with patient outcomes within the initial four-week post-transplantation period.

METHODS: We retrospectively analyzed 41 liver transplant patients with suspected pulmonary infections from August 2022 to May 2023. Bronchoalveolar lavage fluid (BALF) samples were collected on the first postoperative day for metagenomic next generation sequencing (mNGS) and culture. The predictive capability of mNGS for subsequent infections was assessed by monitoring inflammatory biomarkers and comparing the detection rates with culture methods. Real-time Polymerase Chain Reaction (Rt-PCR) was used to monitor Human betaherpesvirus 5 (CMV) and Human parvovirus B19 (B19) weekly during a four-week postoperative period. Inflammatory biomarkers and blood coagulation function were evaluated on specific days throughout the first, third, fifth, and during four weeks following surgery. The study was conducted until August 2023 to evaluate the patients' prognostic survival outcome, classifying them into groups based on the mortality and survival.

RESULTS: The analysis included a total of 41 patients, comprising 32 males and 9 females, with an average age of 52 (47, 63) years. Within one week after liver transplantation, there were 7 cases of bacterial infections, 5 cases of fungal infections, 19 cases of mixed infections, 8 cases without any infection, and 2 cases with unidentified pathogen-associated infections. mNGS successfully predicted 39 (72 %) strains of pathogens, while culture-based methods only detected 28 (52 %) strains. Among the 8 patients diagnosed as non-infected, culture methods identified positive results in 4 cases (50 %), whereas mNGS yielded positive results in 7 cases (87.5 %). The detection rates of CMV and B19 by Rt-PCR within 4 weeks after liver transplantation were 61 % and 17 %, respectively (25/41, 7/41) among the patients. During the study period, a total of 9 patients succumbed while 32 patients survived. The death group and the survival group exhibited significant differences in CRP, HGB, and INR levels at specific monitoring time points. The proportion of CMV detection in blood was significantly higher in the death group compared to the surviving group. Elevated CRP level was identified as a prognostic risk factor.

CONCLUSIONS: Despite the presence of false positives, mNGS still presents a potential advantage in predicting pulmonary infection pathogens following liver transplantation. Furthermore, the levels of CRP and CMV carrier status within four weeks post-surgery exhibit significant associations with patient survival and prognosis.},
}

@article {pmid39253087,
year = {2024},
author = {Huang, Z and Hu, B and Li, J and Feng, M and Wang, Z and Huang, F and Xu, H and Liu, L and Shang, W},
title = {Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1443057},
doi = {10.3389/fimmu.2024.1443057},
pmid = {39253087},
issn = {1664-3224},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Male ; Female ; Adult ; Bacteria/isolation & purification/genetics ; Transplant Recipients ; Aged ; Fungi/isolation & purification/genetics ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs).

METHODS: BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq.

RESULTS: A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined.

CONCLUSION: Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.},
}

Humans
*Kidney Transplantation/adverse effects
*Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Male
Female
Adult
Bacteria/isolation & purification/genetics
Transplant Recipients
Aged
Fungi/isolation & purification/genetics

@article {pmid39252839,
year = {2024},
author = {Murovec, B and Deutsch, L and Stres, B},
title = {Predictive modeling of colorectal cancer using exhaustive analysis of microbiome information layers available from public metagenomic data.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426407},
doi = {10.3389/fmicb.2024.1426407},
pmid = {39252839},
issn = {1664-302X},
abstract = {This study aimed to compare the microbiome profiles of patients with colorectal cancer (CRC, n = 380) and colorectal adenomas (CRA, n = 110) against generally healthy participants (n = 2,461) from various studies. The overarching objective was to conduct a real-life experiment and develop a robust machine learning model applicable to the general population. A total of 2,951 stool samples underwent a comprehensive analysis using the in-house MetaBakery pipeline. This included various data matrices such as microbial taxonomy, functional genes, enzymatic reactions, metabolic pathways, and predicted metabolites. The study found no statistically significant difference in microbial diversity among individuals. However, distinct clusters were identified for healthy, CRC, and CRA groups through linear discriminant analysis (LDA). Machine learning analysis demonstrated consistent model performance, indicating the potential of microbiome layers (microbial taxa, functional genes, enzymatic reactions, and metabolic pathways) as prediagnostic indicators for CRC and CRA. Notable biomarkers on the taxonomy level and microbial functionality (gene families, enzymatic reactions, and metabolic pathways) associated with CRC were identified. The research presents promising avenues for practical clinical applications, with potential validation on external clinical datasets in future studies.},
}

@article {pmid39252828,
year = {2024},
author = {Ng, CWW and Yan, WH and Xia, YT and Tsim, KWK and To, JCT},
title = {Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426893},
doi = {10.3389/fmicb.2024.1426893},
pmid = {39252828},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood.

METHODS: This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm).

RESULTS AND DISCUSSION: It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.},
}

@article {pmid39252782,
year = {2024},
author = {Tan, JH and Liew, KJ and Goh, KM},
title = {Dataset of 313 metagenome-assemble genomes from streamer hot spring water.},
journal = {Data in brief},
volume = {56},
number = {},
pages = {110829},
doi = {10.1016/j.dib.2024.110829},
pmid = {39252782},
issn = {2352-3409},
abstract = {This data report presents prokaryotic metagenome-assembled genomes (MAGs) from a hot spring stream with temperatures between 64 and 100°C. The stream water was filtered and the extracted total DNA was sequenced using the Illumina HiSeq 2500 platform. Approximately 80 Gb of raw data were generated, which were subsequently assembled using MEGAHIT v1.2.9. The MAGs were generated using MetaWRAP with binning approaches of MetaBAT2, CONCOCT and MaxBin2. We constructed 25 medium-quality and 24 high-quality archaeal MAGs, and 152 medium-quality and 112 high-quality bacterial MAGs. The fasta files of these MAGs are available in the NCBI database as well as Mendeley Data. Major phyla identified include Bacteroidota, Chloroflexota, Desulfobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, Verrucomicrobiota, Armatimonadota, Nitrospirota, Acidobacteriota, Elusimicrobiota, Planctomycetota, Candidate division WOR-3, Aquificota, Thermoproteota, and Micrarchaeota. This dataset is valuable for studies on thermophilic genomes, reconstruction of biochemical pathways and gene discovery.},
}

@article {pmid39252128,
year = {2024},
author = {Wu, H and Li, A and Zhang, H and Li, S and Yang, C and Lv, H and Yao, Y},
title = {Microbial mechanisms for higher hydrogen production in anaerobic digestion at constant temperature versus gradient heating.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {170},
pmid = {39252128},
issn = {2049-2618},
mesh = {*Hydrogen/metabolism ; *Lignin/metabolism ; Anaerobiosis ; Hot Temperature ; Cellulose/metabolism ; Polysaccharides/metabolism ; Metagenomics/methods ; Temperature ; Bacteria/metabolism/classification/genetics ; },
abstract = {BACKGROUND: Clean energy hydrogen (H2) produced from abundant lignocellulose is an alternative to fossil energy. As an essential influencing factor, there is a lack of comparison between constant temperatures (35, 55 and 65 °C) and gradient heating temperature (35 to 65 °C) on the H2 production regulation potential from lignocellulose-rich straw via high-solid anaerobic digestion (HS-AD). More importantly, the microbial mechanism of temperature regulating H2 accumulation needs to be investigated.

RESULTS: Constant 65 °C led to the lowest lignin residue (1.93%) and the maximum release of cellulose and hemicellulose, and the highest H2 production (26.01 mL/g VS). H2 production at 35 and 55 °C was only 14.56 and 24.13 mL/g VS, respectively. In order to further explore the potential of ultra-high temperature (65 °C), HS-AD was performed by gradient heating conditions (35 to 65 °C). However, compared to constant 65 °C, gradient heating conditions led to higher lignin residue (2.49%) and lower H2 production (13.53 mL/g VS) than gradient heating conditions (47.98%). In addition, metagenomic analysis showed the cellulose/hemicellulose hydrolyzing bacteria and genes (mainly Thermoclostridium, and xynA, xynB, abfA, bglB and xynD), H2-producing bacteria and related genes (mainly Thermoclostridium, and nifD, nifH and nifK), and microbial movement and metabolic functions were enriched at 65 °C. However, the enrichment of two-component systems under gradient heating conditions resulted in a lack of highly-enriched ultra-high-temperature cellulose/hemicellulose hydrolyzing genera and related genes but rather enriched H2 consumption genera and genes (mainly Acetivibrio, and hyaB and hyaA) resulting in a weaker H2 production.

CONCLUSIONS: The lignin degradation process does not directly determine H2 accumulation, which was actually regulated by bacteria/genes contributing to H2 production/consumption. In addition, it is temperature that enhances the hydrolysis process of lignin rather than lignin-degrading enzymes, bacteria and genes by promoting microbial material transfer and metabolism. In terms of temperature, one of the key parameters of HS-AD for H2 production, we developed an important regulatory strategy, enriched the theoretical basis of temperature regulation for H2 production to further expanded the research horizon in this field. Video Abstract.},
}

*Hydrogen/metabolism
*Lignin/metabolism
Anaerobiosis
Hot Temperature
Cellulose/metabolism
Polysaccharides/metabolism
Metagenomics/methods
Temperature
Bacteria/metabolism/classification/genetics

@article {pmid39252078,
year = {2024},
author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S},
title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {67},
pmid = {39252078},
issn = {2524-6372},
support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; },
abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.},
}

@article {pmid39252069,
year = {2024},
author = {Buddle, S and Forrest, L and Akinsuyi, N and Martin Bernal, LM and Brooks, T and Venturini, C and Miller, C and Brown, JR and Storey, N and Atkinson, L and Best, T and Roy, S and Goldsworthy, S and Castellano, S and Simmonds, P and Harvala, H and Golubchik, T and Williams, R and Breuer, J and Morfopoulou, S and Torres Montaguth, OE},
title = {Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {111},
pmid = {39252069},
issn = {1756-994X},
mesh = {*Metagenomics/methods ; Humans ; *Viruses/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Virus Diseases/diagnosis/virology ; Metagenome ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity.

METHODS: We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.

RESULTS: Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT.

CONCLUSIONS: Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.},
}

*Metagenomics/methods
Humans
*Viruses/genetics/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Virus Diseases/diagnosis/virology
Metagenome
Sensitivity and Specificity

@article {pmid39251745,
year = {2024},
author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M},
title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21034},
pmid = {39251745},
issn = {2045-2322},
support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; },
mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; },
abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.},
}

*Sewage/microbiology
*Soil Microbiology
*Agriculture/methods
*Fertilizers
*Soil/chemistry
*Microbiota/genetics/drug effects
Bacteria/genetics/drug effects/classification
Metagenomics/methods
Drug Resistance, Microbial/genetics
Poland

@article {pmid39251728,
year = {2024},
author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M},
title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21025},
pmid = {39251728},
issn = {2045-2322},
support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; },
mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adolescent ; Multiomics ; },
abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.},
}

Humans
*Hepatolenticular Degeneration/metabolism/microbiology/genetics
*Gastrointestinal Microbiome
Female
Male
Adult
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Feces/microbiology
Metabolome
Young Adult
Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Adolescent
Multiomics

@article {pmid39250478,
year = {2024},
author = {Pusa, T and Rousu, J},
title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0309921},
doi = {10.1371/journal.pone.0309921},
pmid = {39250478},
issn = {1932-6203},
mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.},
}

Humans
*Biomarkers/metabolism
*Inflammatory Bowel Diseases/metabolism
*Metabolomics/methods
Metagenomics/methods
Machine Learning
Gastrointestinal Microbiome
Multiomics

@article {pmid39250184,
year = {2024},
author = {Pallen, MJ},
title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
pmid = {39250184},
issn = {1466-5034},
mesh = {*Bacteria/genetics/classification ; *Phylogeny ; Archaea/genetics/classification ; History, 20th Century ; History, 21st Century ; Prokaryotic Cells/classification ; Classification/methods ; },
abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.},
}

*Bacteria/genetics/classification
*Phylogeny
Archaea/genetics/classification
History, 20th Century
History, 21st Century
Prokaryotic Cells/classification
Classification/methods

@article {pmid39248562,
year = {2024},
author = {Xiao, JZ and Nesbø, CL and Molenda, O and Toth, CRA and Edwards, EA},
title = {Metagenomic and genomic sequences from a nitrate-reducing benzene-degrading enrichment culture.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029424},
doi = {10.1128/mra.00294-24},
pmid = {39248562},
issn = {2576-098X},
abstract = {Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes.},
}

@article {pmid39248477,
year = {2024},
author = {Hu, N-n and Wang, Z-q and Zhang, S-j and Wang, Z-z and Chen, X-x},
title = {Characterization of larval gut microbiota of two endoparasitoid wasps associated with their common host, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0120824},
doi = {10.1128/spectrum.01208-24},
pmid = {39248477},
issn = {2165-0497},
abstract = {Insect gut microbes play important roles in digestion, metabolism, development, and environmental adaptation. Parasitoid wasps are one of the most important biological control agents in pest control, while the gut microbial species compositions and the associated functions have been poorly investigated. Two endoparasitoid wasps, Cotesia vestalis and Diadromus collaris, parasitize the larval stage and pupal stage of the diamondback moth, Plutella xylostella, respectively. Using whole-genome shotgun metagenomic sequencing, we characterized the gut microbial composition, diversity, and potential functional roles associated with the two parasitoid wasp larvae. The results reveal that Proteobacteria and Firmicutes are the dominant phyla in the gut of C. vestalis and D. collaris larvae, with Rhizobium and Enterococcus being the dominant genera. The putative microbial functions associated with the two parasitoid wasps might play a virtual role in assisting in consuming the host's nutritional composition. The enriched CAZymes family genes are primarily involved in the degradation and synthesis of chitin. Despite the richness of microbial species and communities, the microbes species and the microbial community structure exhibit significant similarity between the two parasitoid wasps and between the parasitoid wasp and the host P. xylostella. Notably, the prevalence of the genus Enterococcus shared among them suggests a possible link of gut microbes between the host and their associated parasitoids. Our study offers insights into the gut microbe-based interactions between the host and parasitoid wasps for the first time, potentially paving the way for the development of an ecologically friendly biocontrol strategy against the pest P. xylostella.IMPORTANCEEndoparasitoid wasps spend the majority of their lifespan within their host and heavily rely on the host's nutrition for survival. There is limited understanding regarding the composition and physiological impacts of gut microbial communities in parasitoid wasps, particularly during the larval stage, which is directly linked to the host. Based on a thorough characterization of the gut microbe and comprehensive comparative analysis, we found the microbial species of the larval parasitoid wasp Cotesia vestalis and the pupal parasitoid wasp Diadromus collaris were similar, sharing 159 genera and 277 species, as were the microbial community structure. Certain of the dominant microbial strains of the two parasitoid wasps were similar to that of their host Plutella xylostella larvae, revealing host insect may affect the microbial community of the parasitoid wasps. The putative microbial functions associated with the parasitoid wasp larvae play an important role in dietary consumption.},
}

@article {pmid39248463,
year = {2024},
author = {Zhang, X and Wu, N and Geng, K and Yuan, C and Wang, B and Shi, J and Qiu, J and He, J},
title = {Identification of a chlorosalicylic acid decarboxylase (CsaD) involved in decarboxylation of 3,6-DCSA from an anaerobic dicamba-degrading sludge.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131924},
doi = {10.1128/aem.01319-24},
pmid = {39248463},
issn = {1098-5336},
abstract = {3,6-Dichlorosalicylic acid (3,6-DCSA) is the demethylation metabolite of herbicide 3,6-dichloro-2-methoxy benzoic acid (dicamba). Previous studies have shown that anaerobic sludge further transformed 3,6-DCSA through decarboxylation and dechlorination. However, the anaerobe, enzyme, and gene involved in the anaerobic degradation of 3,6-DCSA are still unknown. In this study, an anaerobic sludge that efficiently degraded dicamba was enriched, and a 3,6-DCSA decarboxylase, designated chlorosalicylic acid decarboxylase (CsaD), was partially purified and identified from the anaerobic sludge. Metagenomic analysis showed that the csaD gene was located in a gene cluster of metagenome-assembled genome 8 (MAG8). MAG8 belonged to an uncultured order, OPB41, in the class Coriobacteriia of the phylum Actinobacteria, and its abundance increased approximately once during the enrichment process. CsaD was a non-oxidative decarboxylase in the amidohydrolase 2 family catalyzing the decarboxylation of 3,6-DCSA and 6-chlorosalicylic acid (6-CSA). Its affinity and catalytic efficiency for 3,6-DCSA were significantly higher than those for 6-CSA. This study provides new insights into the anaerobic catabolism of herbicide dicamba.IMPORTANCEDicamba, an important hormone herbicide, easily migrates to anoxic habitats such as sediment, ground water, and deep soil. Thus, the anaerobic catabolism of dicamba is of importance. Anaerobic bacteria or sludge demethylated dicamba to 3,6-DCSA, and in a previous study, based on metabolite identification, it was proposed that 3,6-DCSA be further degraded via two pathways: decarboxylation to 2,5-dichlorophenol, then dechlorination to 3-chlorophenol (3-CP); or dechlorination to 6-CSA, then decarboxylation to 3-CP. However, there was no physiological and genetic validation for the pathway. In this study, CsaD catalyzed the decarboxylation of both 3,6-DCSA and 6-CSA, providing enzyme-level evidence for the anaerobic catabolism of 3,6-DCSA through the two pathways. CsaD was located in MAG8, which belonged to an uncultured anaerobic actinomycetes order, OPB41, indicating that anaerobic actinomycetes in OPB41 was involved in the decarboxylation of 3,6-DCSA. This study provides a basis for understanding the anaerobic catabolism of dicamba and the demethylation product, 3,6-DCSA.},
}

@article {pmid39248279,
year = {2024},
author = {Ohuchi, H and Asano, R and Mori, A and Ishibashi, T and Motooka, D and Nakai, M and Nakaoka, Y},
title = {Gut Dysbiosis in Patients With Fontan Circulation.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e034538},
doi = {10.1161/JAHA.124.034538},
pmid = {39248279},
issn = {2047-9980},
abstract = {BACKGROUND: The process underlying Fontan pathophysiology is multifactorial and may include gut dysbiosis (GD). We investigated the presence of GD and elucidated its correlation with Fontan pathophysiology.

METHODS AND RESULTS: Gut microbiomes of 155 consecutive patients with Fontan pathophysiology and 44 healthy individuals were analyzed using 16S rRNA sequencing of bacterial DNA extracted from fecal samples. GD was evaluated on the basis of α and ß diversities of the gut microbiome and was compared with natural log-transformed C-reactive protein, hemodynamics, von Willebrand factor antigen (a bacterial translocation marker), Mac-2 binding protein glycosylation isomer (a liver fibrosis indicator), peak oxygen uptake, and heart failure hospitalization. Patients with Fontan exhibited GD in terms of α and ß diversities as compared with controls (P<0.01). Reduced α diversity was associated with a failed hemodynamic phenotype, hypoxia, high natural log-transformed C-reactive protein levels, and elevated von Willebrand factor antigen and Mac-2 binding protein glycosylation isomer levels (P<0.05-0.01). In addition to elevated von Willebrand factor antigen and hypoxia, decreased α diversity was independently correlated with a high natural log-transformed C-reactive protein level (P<0.05), which was associated with liver imaging abnormalities and a heightened risk of heart failure hospitalization (P<0.01 for both).

CONCLUSIONS: Patients with Fontan pathophysiology exhibited GD compared with healthy individuals, and GD was linked to failed hemodynamics and systemic inflammation with a poor prognosis. Therefore, GD may play a pivotal role in a failing Fontan status, including Fontan-associated liver disease, through GD-associated systemic inflammation.},
}

@article {pmid39248272,
year = {2024},
author = {Chen, X and He, Y and Zhou, L and Li, X and Jiang, M and Wu, M and Li, J and Chen, L and Xu, H and Gui, L and Zhou, Z},
title = {Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next-Generation Sequencing-Based Strategy.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e033221},
doi = {10.1161/JAHA.123.033221},
pmid = {39248272},
issn = {2047-9980},
abstract = {BACKGROUND: Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.

METHODS AND RESULTS: Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next-generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large-artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large-artery atherosclerosis showed a significantly higher relative abundance of Ralstonia insidiosa among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.

CONCLUSIONS: This study, based on the approach of metagenomic next-generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large-artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.},
}

@article {pmid39247916,
year = {2024},
author = {Lyu, X and Xu, X and Shen, S and Qin, F},
title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1452999},
pmid = {39247916},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; *Mendelian Randomization Analysis ; *Genome-Wide Association Study ; *Saliva/microbiology ; *Asian People/genetics ; *Microbiota/genetics ; Mouth/microbiology ; Asia, Eastern/epidemiology ; Tongue/microbiology ; Genetic Predisposition to Disease ; East Asian People ; },
abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.

METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).

RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.

DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/genetics
*Mendelian Randomization Analysis
*Genome-Wide Association Study
*Saliva/microbiology
*Asian People/genetics
*Microbiota/genetics
Mouth/microbiology
Asia, Eastern/epidemiology
Tongue/microbiology
Genetic Predisposition to Disease
East Asian People

@article {pmid39247756,
year = {2024},
author = {Lu, Y and Zhang, D and Han, D and Yu, F and Ye, X and Zheng, S},
title = {Case Report: Diagnosis of Hemolytic Anemia from Babesia and Secondary Multi-Pathogen Pneumonia Using a Metagenomic Next-Generation Sequencing Approach.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3785-3791},
pmid = {39247756},
issn = {1178-6973},
abstract = {Babesiosis, as a vector-borne infectious disease, remains relatively rare and is prone to being overlooked and misdiagnosed. Therefore, understanding the epidemiological characteristics and clinical manifestations of babesiosis is crucial for the prompt detection and treatment of the disease. We reported a 63-year-old male patient presenting with spontaneous fever and chills. Laboratory investigations revealed erythrocytopenia, reduced hemoglobin levels, and increased reticulocytes and total bilirubin. Bone marrow examination indicated vigorous cell proliferation, a decreased granulocyte to red cell ratio, and predominant erythroid cell proliferation, with a higher prevalence of intermediate and late-stage juvenile granulocyte and erythroid cells. Initial treatment focused on hemophagocytic syndrome triggered by Epstein-Barr virus infection yielded unsatisfactory results, leading to secondary multiple pulmonary infections. Metagenomic next-generation sequencing (mNGS) of sputum samples pointed to hemolytic anemia induced by Babesia infection, which was subsequently confirmed through peripheral blood smear analysis. The patient responded well to prompt administration of atovaquone and azithromycin, with symptoms resolving and laboratory parameters normalizing. Hemolytic anemia resulting from babesiosis should be distinguished from hemophagocytic syndrome caused by Epstein-Barr virus and other hematologic conditions. mNGS represents an efficient technique for Babesia detection.},
}

@article {pmid39247454,
year = {2024},
author = {Rajguru, B and Shri, M and Bhatt, VD},
title = {Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.},
journal = {3 Biotech},
volume = {14},
number = {10},
pages = {224},
pmid = {39247454},
issn = {2190-572X},
abstract = {The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.},
}

@article {pmid39246231,
year = {2024},
author = {Du, Y and Zuo, W and Sun, F},
title = {Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0663},
pmid = {39246231},
issn = {1557-8666},
abstract = {Metagenomic Hi-C (metaHi-C) has shown remarkable potential for retrieving high-quality metagenome-assembled genomes from complex microbial communities. Nevertheless, existing metaHi-C-based contig binning methods solely rely on Hi-C interactions between contigs, disregarding crucial biological information such as the presence of single-copy marker genes. To overcome this limitation, we introduce ImputeCC, an integrative contig binning tool optimized for metaHi-C datasets. ImputeCC integrates both Hi-C interactions and the discriminative power of single-copy marker genes to group marker-gene-containing contigs into preliminary bins. It also introduces a novel constrained random walk with restart algorithm to enhance Hi-C connectivity among contigs. Comprehensive assessments using both mock and real metaHi-C datasets from diverse environments demonstrate that ImputeCC consistently outperforms other Hi-C-based contig binning tools. A genus-level analysis of the sheep gut microbiota reconstructed by ImputeCC underlines its capability to recover key species from dominant genera and identify previously unknown genera.},
}

@article {pmid39245657,
year = {2024},
author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {80},
pmid = {39245657},
issn = {2055-5008},
support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation & purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; },
abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.},
}

*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Humans
*Metagenomics/methods
Sweden
*Bacteria/classification/genetics/isolation & purification
*Feces/microbiology
Longitudinal Studies
Metagenome
Adult
Bioreactors/microbiology
Fermentation

@article {pmid39245322,
year = {2024},
author = {Jiménez, JD and Godoy, MS and Del Cerro, C and Prieto, MA},
title = {Hints from nature for a PHA circular economy: carbon synthesis and sharing by Pseudomonas solani GK13.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2024.09.002},
pmid = {39245322},
issn = {1876-4347},
abstract = {Polyhydroxyalkanoates (PHAs) are a well-known group of biodegradable and biocompatible bioplastics that are synthesised and stored by microorganisms as carbon and energy reservoirs. Extracellular PHA depolymerases (ePhaZs), secreted by a limited range of microorganisms, are the main hydrolytic enzymes responsible for their environmental degradation. Pseudomonas sp. GK13, initially identified as P. fluorescens GK13, produces PHA and a prototypic ePhaZ that specifically degrades mcl-PHA. In this study, a comprehensive characterization of strain GK13 was performed. The whole genomic sequence of GK13 was consolidated into one complete chromosome, leading to its reclassification as P. solani GK13. We conducted a detailed in silico examination of the bacteria genomic sequence, specifically targeting PHA metabolic functions. From the different growth conditions explored, PHA accumulation occurred only under carbon/nitrogen (C/N) imbalance, whereas ePhaZ production was induced even at balanced C/N ratios in mineral media. We extend our study to other bacteria belonging to the Pseudomonas genus revealing that the ePhaZ production capacity is closely associated with mcl-PHA synthesis capacity, as also suggested by metagenomic samples. This finding suggests that these types of microorganisms could contribute to the carbon economy of the microbial community, by storing PHA in carbon-rich times, and sharing it with the community during times of carbon scarcity through PHA hydrolysis. The conclusion pointed that carbon cycle metabolism performed by P. solani GK13 may contribute to the environmental circular economy at a microscopic scale.},
}

@article {pmid39245190,
year = {2024},
author = {Huang, J and Liu, S and Li, P and Wei, L and Lin, G and Lin, J and Luo, Y and Liu, Y and Mao, Y and Ruan, H and Qin, B and Fan, P and Lu, T and Cai, W and Yi, H and Mou, X and Lu, Z and Zhao, W and Wu, A},
title = {Multi-Omics Analysis of Gut-Brain Axis Reveals Novel Microbial and Neurotransmitter Signatures in Patients with Arteriosclerotic Cerebral Small Vessel Disease.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107385},
doi = {10.1016/j.phrs.2024.107385},
pmid = {39245190},
issn = {1096-1186},
abstract = {Arteriosclerotic cerebral small vessel disease (aCSVD) is a major cause of stroke and dementia. Although its underlying pathogenesis remains poorly understood, both inflammaging and gut microbiota dysbiosis have been hypothesized to play significant roles. This study investigated the role of gut microbiota in the pathogenesis of aCSVD through a comparative analysis of the gut microbiome and metabolome between CSVD patients and healthy controls. The results showed that patients with aCSVD exhibited a marked reduction in potentially beneficial bacterial species, such as Faecalibacterium prausnitzli and Roseburia intestinalis, alongside an increase in taxa from Bacteroides and Proteobacteria. Integrated metagenomic and metabolomic analyses revealed that alterations in microbial metabolic pathways, including LPS biosynthesis and phenylalanine-tyrosine metabolism, were associated with the status of aCSVD. Our findings indicated that microbial LPS biosynthesis and phenylalanine-tyrosine metabolism potentially influenced the symptoms and progression of aCSVD via pro-inflammatory effect and modulation of systemic neurotransmitters, respectively. These results imply that gut microbiota characteristics may serve as indicators for early detection of aCSVD and as potential gut-directed therapeutic intervention target.},
}

@article {pmid39245157,
year = {2024},
author = {Zhang, L and Xu, W and Zhao, Y and Sui, L and Song, M and Liu, Q},
title = {Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107378},
doi = {10.1016/j.actatropica.2024.107378},
pmid = {39245157},
issn = {1873-6254},
abstract = {Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.},
}

@article {pmid39244980,
year = {2024},
author = {Zhao, S and Zhang, Q and Huang, Q and Zhang, C and Li, H and Siddique, KHM},
title = {Polyvinyl chloride microplastics disseminate antibiotic resistance genes in Chinese soil: A metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135727},
doi = {10.1016/j.jhazmat.2024.135727},
pmid = {39244980},
issn = {1873-3336},
abstract = {The widespread prevalence of microplastics (MPs) in the environment poses concerns as they are vectors of antibiotic resistance genes (ARGs). The relationships between antibiotic resistomes and MPs remain unexplored in soil which was considered as the reservoirs of MPs and ARGs. This study investigated the effects of polyvinyl chloride (PVC) MPs on soil bacterial communities and ARG abundance which soil samples sourced from 20 provinces across China. We found that PVC significantly influences soil bacterial community structure and ARG abundance. Structural equation modeling revealed that PVC alters soil characteristics, ultimately affecting soil bacterial communities, including ARG-containing bacterial hosts, and the relative abundance of ARGs. This study enhances our understanding of how MPs influence the proliferation and hosts of ARGs within diverse soil environments, offering crucial insights for future strategies in plastic management and disposal.},
}