@article {pmid39720963,
year = {2024},
author = {Guha, SK and Niyogi, S},
title = {Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.},
journal = {Current microbiology},
volume = {82},
number = {1},
pages = {59},
pmid = {39720963},
issn = {1432-0991},
mesh = {Humans ; *COVID-19/microbiology/virology ; *SARS-CoV-2 ; *Microbiota ; *Dysbiosis/microbiology ; Disease Susceptibility ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; },
abstract = {This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.},
}

Humans
*COVID-19/microbiology/virology
*SARS-CoV-2
*Microbiota
*Dysbiosis/microbiology
Disease Susceptibility
Probiotics/therapeutic use
Gastrointestinal Microbiome

@article {pmid39673707,
year = {2024},
author = {Huang, KD and Müller, M and Sivapornnukul, P and Bielecka, AA and Amend, L and Tawk, C and Lesker, TR and Hahn, A and Strowig, T},
title = {Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115067},
doi = {10.1016/j.celrep.2024.115067},
pmid = {39673707},
issn = {2211-1247},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Adult ; Male ; Bacteria/genetics/classification ; Female ; Genetic Variation ; Middle Aged ; },
abstract = {Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diet
Adult
Male
Bacteria/genetics/classification
Female
Genetic Variation
Middle Aged

@article {pmid39615045,
year = {2024},
author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D},
title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115018},
doi = {10.1016/j.celrep.2024.115018},
pmid = {39615045},
issn = {2211-1247},
mesh = {Humans ; *Ruminococcus/genetics ; *Life Style ; Genome, Bacterial ; Adult ; Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; Genomics/methods ; Male ; Middle Aged ; Female ; Aged ; },
abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.},
}

Humans
*Ruminococcus/genetics
*Life Style
Genome, Bacterial
Adult
Gastrointestinal Microbiome/genetics
Metagenome
Phylogeny
Genomics/methods
Male
Middle Aged
Female
Aged

@article {pmid39602306,
year = {2024},
author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D},
title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115027},
doi = {10.1016/j.celrep.2024.115027},
pmid = {39602306},
issn = {2211-1247},
mesh = {Humans ; *Phylogeny ; *Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Genome-Wide Association Study ; Probiotics ; },
abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.},
}

Humans
*Phylogeny
*Microbiota/genetics
Metagenome
Genome, Bacterial
Genome-Wide Association Study
Probiotics

@article {pmid39719433,
year = {2024},
author = {Jia, M and Fan, Y and Ma, Q and Yang, D and Wang, Y and He, X and Zhao, B and Zhan, X and Qi, Z and Ren, Y and Dong, Z and Zhu, F and Wang, W and Gao, Y and Ma, X},
title = {Gut microbiota dysbiosis promotes cognitive impairment via bile acid metabolism in major depressive disorder.},
journal = {Translational psychiatry},
volume = {14},
number = {1},
pages = {503},
pmid = {39719433},
issn = {2158-3188},
support = {82230044//National Science Foundation of China | Key Programme/ ; 82171505//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Depressive Disorder, Major/metabolism/microbiology ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Dysbiosis/metabolism/complications ; *Cognitive Dysfunction/metabolism/etiology/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; Brain-Gut Axis ; },
abstract = {Evidence suggests that complex interactions among the gut microbiome, metabolic abnormalities, and brain have important etiological and therapeutic implications in major depressive disorder (MDD). However, the influence of microbiome-gut-brain cross-talk on cognitive impairment in MDD remains poorly characterized. We performed serum metabolomic profiling on 104 patients with MDD and 77 healthy controls (HCs), and also performed fecal metagenomic sequencing on a subset of these individuals, including 79 MDD patients and 60 HCs. The findings were validated in a separate cohort that included 40 patients with MDD and 40 HCs using serum-targeted metabolomics. Abnormal bile acid metabolism was observed in patients with MDD, which is related to cognitive dysfunction. The following gut microbiota corresponded to changes in bile acid metabolism and enzyme activities involved in the bile acid metabolic pathway, including Lachnospiraceae (Blautia_massiliensis, Anaerostipes_hadrus, Dorea_formicigenerans, and Fusicatenibacter_saccharivorans), Ruminococcaceae (Ruminococcus_bromii, Flavonifractor_plautii, and Ruthenibacterium_lactatiformans), and Escherichia_coli. Furthermore, a combinatorial marker classifier that robustly differentiated patients with MDD from HCs was identified. In conclusion, this study provides insights into the gut-brain interactions in the cognitive phenotype of MDD, indicating a potential therapeutic strategy for MDD-associated cognitive impairment by targeting the gut microbiota and bile acid metabolism.},
}

Humans
*Gastrointestinal Microbiome
*Depressive Disorder, Major/metabolism/microbiology
*Bile Acids and Salts/metabolism
Male
Female
*Dysbiosis/metabolism/complications
*Cognitive Dysfunction/metabolism/etiology/microbiology
Adult
Middle Aged
Feces/microbiology
Metabolomics
Case-Control Studies
Brain-Gut Axis

@article {pmid39716092,
year = {2024},
author = {Chapman, JA and Wroot, E and Brown, T and Beck, LC and Embleton, ND and Berrington, JE and Stewart, CJ},
title = {Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {533},
pmid = {39716092},
issn = {1471-2180},
mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/metabolism ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; Bacteria/classification/metabolism/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; Metagenome ; },
abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.

RESULTS: Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.

CONCLUSIONS: Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.},
}

Humans
*Enterocolitis, Necrotizing/microbiology/metabolism
*Gastrointestinal Microbiome
Pilot Projects
Infant, Newborn
*Infant, Premature
Female
Male
Bacteria/classification/metabolism/isolation & purification/genetics
Feces/microbiology
Case-Control Studies
Metagenome

@article {pmid39716039,
year = {2025},
author = {Du, Q and Liu, X and Zhang, R and Hu, G and Liu, Q and Wang, R and Ma, W and Hu, Y and Fan, Z and Li, J},
title = {Placental and Fetal Microbiota in Rhesus Macaque: A Case Study Using Metagenomic Sequencing.},
journal = {American journal of primatology},
volume = {87},
number = {1},
pages = {e23718},
doi = {10.1002/ajp.23718},
pmid = {39716039},
issn = {1098-2345},
support = {//This work was supported by the National Natural Science Foundation of China (32171607)/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; Female ; Pregnancy ; *Fetus/microbiology ; *Placenta/microbiology ; *Microbiota ; *Metagenomics ; Umbilical Cord/microbiology ; Gastrointestinal Microbiome ; },
abstract = {Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.},
}

Animals
*Macaca mulatta/microbiology
Female
Pregnancy
*Fetus/microbiology
*Placenta/microbiology
*Microbiota
*Metagenomics
Umbilical Cord/microbiology
Gastrointestinal Microbiome

@article {pmid38686914,
year = {2025},
author = {Spatola Rossi, T and Gallia, M and Erijman, L and Figuerola, E},
title = {Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant.},
journal = {Environmental technology},
volume = {46},
number = {1},
pages = {135-150},
doi = {10.1080/09593330.2024.2343797},
pmid = {38686914},
issn = {1479-487X},
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Waste Disposal, Fluid/methods ; Sewage/microbiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.},
}

*Bioreactors/microbiology
Anaerobiosis
*Archaea/metabolism/genetics
*Wastewater/microbiology
*Bacteria/metabolism/genetics/classification
Waste Disposal, Fluid/methods
Sewage/microbiology
Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid39715919,
year = {2024},
author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL},
title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {162},
pmid = {39715919},
issn = {1432-184X},
support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; },
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyll/analysis ; },
abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.},
}

*Soil/chemistry
*Soil Microbiology
*Bryophyta/microbiology
China
Biodiversity
Alkalies/analysis
Salinity
Bacteria/classification/genetics/isolation & purification/metabolism
Chlorophyll/analysis

@article {pmid39714548,
year = {2024},
author = {Wang, W and Zhang, Z and Sun, M and Li, C and Yan, M and Wang, C},
title = {Mechanism of decolorization and degradation of direct brown D3G by a halo-thermophilic consortium.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {11},
pmid = {39714548},
issn = {1433-4909},
support = {22B610001//the Key Scientific Research Project in Colleges and Universities of Henan Province of China/ ; HDXJJG2023-058//the teaching reform project of Henan University/ ; },
mesh = {*Azo Compounds/metabolism/chemistry ; Microbial Consortia ; Biodegradation, Environmental ; Halomonas/metabolism ; Coloring Agents/metabolism/chemistry ; Laccase/metabolism ; Bacillus/metabolism ; },
abstract = {Azo dye wastewater has garnered significant attention from researchers because of its association with high-temperature, high-salt, and high-alkali conditions. In this study, consortium ZZ efficiently decolorized brown D3G under halophilic and thermophilic conditions. he results indicated that consortium ZZ, which was mainly dominated by Marinobacter, Bacillus, and Halomonas, was achieved decolorization rates ranging from 1 to 10% at temperatures between 40 °C and 50 °C, while maintaining a pH range of 7 to 10 for direct brown D3G degradation. Through the comprehensive utilization of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS) techniques, as well as metagenomic analysis, the decolorization and degradation pathway of direct brown by consortium ZZ was proposed. The azo dye reductase, lignin peroxidase, and laccase were also highly expressed in the decolorization process. Additionally, phytotoxicity tests using seeds of Cucumis sativus and Oryza sativa revealed that the intermediates generated showed no significant toxicity compared with distilled water. This investigation elucidated the pivotal contribution of consortium ZZ to azo dye degradation and provided novel theoretical insights along with practical guidance for azo dye treatment at halo-thermophilic conditions.},
}

*Azo Compounds/metabolism/chemistry
Microbial Consortia
Biodegradation, Environmental
Halomonas/metabolism
Coloring Agents/metabolism/chemistry
Laccase/metabolism
Bacillus/metabolism

@article {pmid39713824,
year = {2024},
author = {Karesh, WB},
title = {Shifting from wildlife disease threats to wildlife health.},
journal = {Revue scientifique et technique (International Office of Epizootics)},
volume = {Special Edition},
number = {},
pages = {141-144},
doi = {10.20506/rst.SE.3568},
pmid = {39713824},
issn = {0253-1933},
mesh = {Animals ; *Animals, Wild ; Humans ; Zoonoses/prevention & control ; Conservation of Natural Resources ; Animal Diseases/prevention & control/epidemiology ; },
abstract = {The evolution of wildlife disease management and surveillance, as documented in the World Organisation for Animal Health's Scientific and Technical Review, reflects a deepening understanding of the links between wildlife health, ecosystem integrity and human well-being. Early work, beginning with the World Assembly of Delegates in 1954, primarily focused on diseases like rabies. This focus expanded over time to include broader concerns such as the impacts of climate change, habitat loss and increased human-wildlife interactions on wildlife health. By the late 20th century, the emphasis had shifted towards improved practices for wildlife disease control and the development of advanced diagnostic methods and vaccines. Articles in the Review highlight the growing complexity of wildlife diseases and the need for holistic management strategies. The adoption in recent years of cutting-edge technologies like CRISPR-Cas systems and metagenomics points to a future of more proactive and integrated approaches to wildlife disease management. There is still a need to address not just the consequences of wildlife diseases but also their anthropogenic drivers. The latest perspectives advocate for nature-based solutions, expanded partnerships and systems-level thinking to effectively tackle 21st-century challenges in wildlife and biodiversity conservation.},
}

Animals
*Animals, Wild
Humans
Zoonoses/prevention & control
Conservation of Natural Resources
Animal Diseases/prevention & control/epidemiology

@article {pmid39711113,
year = {2025},
author = {Olivares, C and Ruppé, E and Ferreira, S and Corbel, T and Andremont, A and de Gunzburg, J and Guedj, J and Burdet, C},
title = {A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2442523},
doi = {10.1080/19490976.2024.2442523},
pmid = {39711113},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Ceftazidime/pharmacology/administration & dosage ; Male ; Moxifloxacin/pharmacology/administration & dosage ; Drug Combinations ; Ceftriaxone/pharmacology/administration & dosage ; Female ; Azabicyclo Compounds/pharmacology/administration & dosage ; Biodiversity ; Young Adult ; Healthy Volunteers ; Piperacillin, Tazobactam Drug Combination ; },
abstract = {Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Feces/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification
*RNA, Ribosomal, 16S/genetics
Adult
Ceftazidime/pharmacology/administration & dosage
Male
Moxifloxacin/pharmacology/administration & dosage
Drug Combinations
Ceftriaxone/pharmacology/administration & dosage
Female
Azabicyclo Compounds/pharmacology/administration & dosage
Biodiversity
Young Adult
Healthy Volunteers
Piperacillin, Tazobactam Drug Combination

@article {pmid39709594,
year = {2025},
author = {Smith, MZ and York, M and Townsend, KS and Martin, LM and Gull, T and Coghill, LM and Ericsson, AC and Johnson, PJ},
title = {Effects of orally administered clioquinol on the fecal microbiome of horses.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {1},
pages = {e17276},
doi = {10.1111/jvim.17276},
pmid = {39709594},
issn = {1939-1676},
mesh = {Animals ; Horses ; *Feces/microbiology ; *Clioquinol/pharmacology/administration & dosage ; Female ; Male ; Administration, Oral ; Prospective Studies ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {BACKGROUND: Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.

OBJECTIVES: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.

STUDY DESIGN: Experimental prospective cohort study using a single horse group.

METHODS: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).

RESULTS: The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.

MAIN LIMITATIONS: Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.

CONCLUSIONS: Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.},
}

Animals
Horses
*Feces/microbiology
*Clioquinol/pharmacology/administration & dosage
Female
Male
Administration, Oral
Prospective Studies
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Cohort Studies

@article {pmid39709449,
year = {2024},
author = {Dos Santos, SJ and Copeland, C and Macklaim, JM and Reid, G and Gloor, GB},
title = {Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {271},
pmid = {39709449},
issn = {2049-2618},
support = {20170705//Weston Family Foundation/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; *Microbiota/genetics ; *Transcriptome ; *Bacteria/genetics/classification/isolation & purification ; Biofilms/growth & development ; Metagenomics/methods ; },
abstract = {BACKGROUND: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.

RESULTS: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).

CONCLUSIONS: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.},
}

Humans
Female
*Vagina/microbiology
*Vaginosis, Bacterial/microbiology
*Microbiota/genetics
*Transcriptome
*Bacteria/genetics/classification/isolation & purification
Biofilms/growth & development
Metagenomics/methods

@article {pmid39708838,
year = {2024},
author = {Luo, Q and Zhang, S and Butt, H and Chen, Y and Jiang, H and An, L},
title = {PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbae653},
pmid = {39708838},
issn = {1477-4054},
support = {R01ES027013//National Institute of Health/ ; ARZT-1361620-H22-149//United States Department of Agriculture/ ; },
mesh = {*Phylogeny ; Algorithms ; Humans ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Sequencing-based microbial count data analysis is a challenging task due to the presence of numerous non-biological zeros, which can impede downstream analysis. To tackle this issue, we introduce two novel approaches, PhyImpute and UniFracImpute, which leverage similar microbial samples to identify and impute non-biological zeros in microbial count data. Our proposed methods utilize the probability of non-biological zeros and phylogenetic trees to estimate sample-to-sample similarity, thus addressing this challenge. To evaluate the performance of our proposed methods, we conduct experiments using both simulated and real microbial data. The results demonstrate that PhyImpute and UniFracImpute outperform existing methods in recovering the zeros and empowering downstream analyses such as differential abundance analysis, and disease status classification.},
}

*Phylogeny
Algorithms
Humans
Computational Biology/methods
Microbiota/genetics

@article {pmid39707929,
year = {2024},
author = {Shahzaib, M and Muaz, M and Zubair, MH and Kayani, MUR},
title = {MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
doi = {10.1093/database/baae124},
pmid = {39707929},
issn = {1758-0463},
mesh = {Humans ; *Neoplasms/genetics/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Neoplasm/genetics ; *Databases, Genetic ; },
abstract = {Cancer remains a global health challenge, with significant morbidity and mortality rates. In 2020, cancer caused nearly 10 million deaths, making it the second leading cause of death worldwide. The emergence of chemoresistance has become a major hurdle in successfully treating cancer patients. Recently, human gut microbes have been recognized for their role in modulating drug efficacy through their metabolites, ultimately leading to chemoresistance. The currently available databases are limited to knowledge regarding the interactions between gut microbiome and drugs. However, a database containing the human gut microbial gene sequences, and their effect on the efficacy of chemotherapy for cancer patients has not yet been developed. To address this challenge, we present the Microbial Chemoresistance Knowledgebase (MiCK), a comprehensive database that catalogs microbial gene sequences associated with chemoresistance. MiCK contains 1.6 million sequences of 29 gene types linked to chemoresistance and drug metabolism, curated manually from recent literature and sequence databases. The database can support downstream analysis as it provides a user-friendly web interface for sequence search and download functionalities. MiCK aims to facilitate the understanding and mitigation of chemoresistance in cancers by serving as a valuable resource for researchers. Database URL: https://microbialchemreskb.com/.},
}

Humans
*Neoplasms/genetics/drug therapy
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Neoplasm/genetics
*Databases, Genetic

@article {pmid39707568,
year = {2024},
author = {Yang, X and Yuan, R and Yang, S and Dai, Z and Di, N and Yang, H and He, Z and Wei, M},
title = {A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {270},
pmid = {39707568},
issn = {2049-2618},
mesh = {*Oryza/microbiology/growth & development ; *Salt Tolerance ; *Plant Leaves/microbiology ; Microbiota ; Rhizosphere ; Pantoea/genetics ; Soil Microbiology ; Bacillus/genetics/isolation & purification/physiology ; Bacteria/genetics/classification/isolation & purification ; Wetlands ; Rhizophoraceae/microbiology ; Quorum Sensing ; },
abstract = {BACKGROUND: Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.

RESULTS: In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.

CONCLUSIONS: This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.},
}

*Oryza/microbiology/growth & development
*Salt Tolerance
*Plant Leaves/microbiology
Microbiota
Rhizosphere
Pantoea/genetics
Soil Microbiology
Bacillus/genetics/isolation & purification/physiology
Bacteria/genetics/classification/isolation & purification
Wetlands
Rhizophoraceae/microbiology
Quorum Sensing

@article {pmid39707567,
year = {2024},
author = {Feng, X and Xing, P and Tao, Y and Wang, X and Wu, QL and Liu, Y and Luo, H},
title = {Functional traits and adaptation of lake microbiomes on the Tibetan Plateau.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {264},
pmid = {39707567},
issn = {2049-2618},
support = {2023A1515012162//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022M712195//the China Postdoctoral Science Foundation/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U2102216//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; AoE/M-403/16//the Hong Kong Research Grants Council Area of Excellence Scheme/ ; },
mesh = {*Lakes/microbiology ; Tibet ; *Microbiota/genetics ; *Phylogeny ; *Bacteria/classification/genetics ; Metagenome ; Salinity ; Climate Change ; Ecosystem ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.

RESULTS: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.

CONCLUSIONS: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.},
}

*Lakes/microbiology
Tibet
*Microbiota/genetics
*Phylogeny
*Bacteria/classification/genetics
Metagenome
Salinity
Climate Change
Ecosystem
Adaptation, Physiological

@article {pmid39707560,
year = {2024},
author = {Wang, H and Sun, C and Li, Y and Chen, J and Zhao, XM and Chen, WH},
title = {Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {260},
pmid = {39707560},
issn = {2049-2618},
support = {T2225015//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; },
mesh = {*Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology ; Metagenomics/methods ; Virome/genetics ; Viruses/genetics/classification ; Benchmarking ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.

RESULTS: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.

CONCLUSIONS: Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.},
}

*Genome, Viral/genetics
Humans
*High-Throughput Nucleotide Sequencing/methods
*Gastrointestinal Microbiome/genetics
*Metagenome/genetics
*Feces/virology
Metagenomics/methods
Virome/genetics
Viruses/genetics/classification
Benchmarking
Sequence Analysis, DNA/methods

@article {pmid39707557,
year = {2024},
author = {Santamarina-García, G and Yap, M and Crispie, F and Amores, G and Lordan, C and Virto, M and Cotter, PD},
title = {Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {262},
pmid = {39707557},
issn = {2049-2618},
support = {IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; PIF19/31//Euskal Herriko Unibertsitatea/ ; },
mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota ; *Metagenomics ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Dairying ; Food Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS: The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION: This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.},
}

*Cheese/microbiology
Animals
*Milk/microbiology
*Microbiota
*Metagenomics
Sheep/microbiology
*Bacteria/classification/genetics/isolation & purification
Female
Dairying
Food Microbiology
Metagenome

@article {pmid39707494,
year = {2024},
author = {Li, C and Liu, K and Gu, C and Li, M and Zhou, P and Chen, L and Sun, S and Li, X and Wang, L and Ni, W and Li, M and Hu, S},
title = {Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {268},
pmid = {39707494},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral/genetics ; *NAD/metabolism ; *Phylogeny ; Humans ; Gastrointestinal Microbiome ; Swine ; Sheep ; Metagenomics ; Horses ; Cattle ; Bacteria/virology/genetics ; Deer/virology ; DNA Replication ; },
abstract = {BACKGROUND: Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.

RESULTS: In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD[+] by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD[+], these NAD-jumbo phages also encode at least 15 types of NAD[+]-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD[+] but also redirect NAD[+] metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.

CONCLUSION: In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.},
}

*Bacteriophages/genetics/classification/isolation & purification
Animals
*Genome, Viral/genetics
*NAD/metabolism
*Phylogeny
Humans
Gastrointestinal Microbiome
Swine
Sheep
Metagenomics
Horses
Cattle
Bacteria/virology/genetics
Deer/virology
DNA Replication

@article {pmid39707478,
year = {2024},
author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J},
title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {259},
pmid = {39707478},
issn = {2049-2618},
mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; },
abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.

RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.

CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.},
}

*Methane/metabolism
*Soil Microbiology
*Soil/chemistry
*Oryza/microbiology
Microbiota
Polyethylene
Soil Pollutants
Metagenomics
Archaea/metabolism/genetics/classification
Carbon/metabolism
Plastics

@article {pmid39706917,
year = {2024},
author = {Chang, WS and Harvey, E and Mahar, JE and Firth, C and Shi, M and Simon-Loriere, E and Geoghegan, JL and Wille, M},
title = {Improving the reporting of metagenomic virome-scale data.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1687},
pmid = {39706917},
issn = {2399-3642},
mesh = {*Virome/genetics ; *Metagenomics/methods ; Humans ; Animals ; *Viruses/genetics/classification ; Metagenome ; Genome, Viral ; },
abstract = {Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.},
}

*Virome/genetics
*Metagenomics/methods
Humans
Animals
*Viruses/genetics/classification
Metagenome
Genome, Viral

@article {pmid39705954,
year = {2024},
author = {Basile, A and Riggio, FP and Tescari, M and Chebbi, A and Sodo, A and Bartoli, F and Imperi, F and Caneva, G and Visca, P},
title = {Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178135},
doi = {10.1016/j.scitotenv.2024.178135},
pmid = {39705954},
issn = {1879-1026},
abstract = {Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.},
}

@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; },
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}

*Bacteriophages/genetics
*Particulate Matter
China
*Bacteria/genetics/drug effects
*Seasons
Humans
Air Microbiology
Cities
Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Air Pollutants/analysis
Metagenomics
Drug Resistance, Bacterial/genetics
Microbiota

@article {pmid39705480,
year = {2024},
author = {Lu, S and Sun, L and Cao, L and Zhao, M and Guo, Y and Li, M and Duan, S and Zhai, Y and Zhang, X and Wang, Y and Gai, W and Cui, X},
title = {Analysis of lung microbiota in pediatric pneumonia patients using BALF metagenomic next-generation sequencing: A retrospective observational study.},
journal = {Medicine},
volume = {103},
number = {51},
pages = {e40860},
doi = {10.1097/MD.0000000000040860},
pmid = {39705480},
issn = {1536-5964},
support = {202139//Clinical Medical peronnel training programs/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Child, Preschool ; Child ; *Lung/microbiology ; *Microbiota/genetics ; Infant ; Metagenomics/methods ; Severity of Illness Index ; Pneumonia/microbiology ; Pneumonia, Mycoplasma/microbiology/diagnosis ; },
abstract = {The contribution of the lung microbiota to pneumonia in children of varying severity remains poorly understood. This study utilized metagenomic next-generation sequencing (mNGS) technology to elucidate the characteristics of lung microbiota and their association with disease severity. This retrospective study analyzed bronchoalveolar lavage fluid (BALF) mNGS data of 92 children diagnosed with pneumonia between January 2021 and July 2022. A comparative analysis of the lung microbiota was conducted between the severe pneumonia (SP) (n = 44) and non-severe pneumonia (NSP) (n = 48) groups. Compared to conventional microbiological tests (CMT), mNGS had a higher positivity rate in etiology detection (68% vs 100%). In the NSP group, the predominant type of infection was Mycoplasma pneumoniae single infection, whereas in the SP group, the main type involved a combination of M pneumoniae and bacterial infection. The top 3 identified microbial taxa in both the groups were M pneumoniae, Rothia mucilaginosa, and Schaalia odontolyticus. Although there were no significant differences in the α and β diversity of the lung microbiota between the SP and NSP groups, the abundance of M pneumoniae was higher in the SP group (P = .053). Spearman analysis indicated a highly significant positive correlation between the abundance of Prevotella melaninogenica and M pneumoniae (P < .001). Our analysis identified an association between M pneumoniae infections and disease severity. This study provides a foundation for a better understanding of the pathogenesis of pediatric pneumonia and the relationship between microorganisms.},
}

Humans
Retrospective Studies
Male
Female
*Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
Child, Preschool
Child
*Lung/microbiology
*Microbiota/genetics
Infant
Metagenomics/methods
Severity of Illness Index
Pneumonia/microbiology
Pneumonia, Mycoplasma/microbiology/diagnosis

@article {pmid39705298,
year = {2024},
author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM},
title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.},
journal = {Environmental microbiology},
volume = {26},
number = {12},
pages = {e70008},
doi = {10.1111/1462-2920.70008},
pmid = {39705298},
issn = {1462-2920},
support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; },
mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; },
abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.},
}

*Coral Reefs
Animals
*Anthozoa/microbiology
*Bacteria/genetics/classification
*Microbiota
Virulence Factors/genetics

@article {pmid39702650,
year = {2024},
author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH},
title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {152},
pmid = {39702650},
issn = {2055-5008},
support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; },
abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.},
}

*Gastrointestinal Microbiome
Humans
Female
*Machine Learning
Male
Middle Aged
*Menopause
Aged
Sex Factors
Metagenomics/methods
Adult
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Feces/microbiology

@article {pmid39702405,
year = {2024},
author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S},
title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1663},
pmid = {39702405},
issn = {2399-3642},
mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; },
abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.},
}

Oregon
*Microbiota/genetics
*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenomics/methods
Biodiversity

@article {pmid39702006,
year = {2024},
author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A},
title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1224},
pmid = {39702006},
issn = {1471-2164},
mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; },
abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.},
}

*DNA Methylation
*Gastrointestinal Microbiome/genetics
Humans
*Epigenome
*Genome-Wide Association Study
Male
Female
RNA, Ribosomal, 16S/genetics
CpG Islands/genetics
Middle Aged
Adult
Netherlands

@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@article {pmid39626421,
year = {2024},
author = {Wang, J and Wu, D and Wu, Q and Chen, J and Zhao, Y and Wang, H and Liu, F and Yuan, Q},
title = {Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177782},
doi = {10.1016/j.scitotenv.2024.177782},
pmid = {39626421},
issn = {1879-1026},
mesh = {China ; *Lakes/microbiology/chemistry ; *Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; Methylococcaceae/genetics/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Microbiota ; },
abstract = {Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g[-1] d[-1], which was higher than that in reservoirs sediment (1.92 to 11.56 μg g[-1] d[-1]). Similarly, the average AeOM in the water column of lake (104.7 μg L[-1] d[-1]) was much higher than that of reservoirs (46 μg L[-1] d[-1]). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.},
}

China
*Lakes/microbiology/chemistry
*Methane/metabolism/analysis
*Geologic Sediments/microbiology/chemistry
Methylococcaceae/genetics/metabolism
Oxidation-Reduction
RNA, Ribosomal, 16S
Environmental Monitoring
Microbiota

@article {pmid39577582,
year = {2024},
author = {Mukherjee, S and Bhattacharya, R and Sarkar, O and Islam, S and Biswas, SR and Chattopadhyay, A},
title = {Gut microbiota perturbation and subsequent oxidative stress in gut and kidney tissues of zebrafish after individual and combined exposure to inorganic arsenic and fluoride.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177519},
doi = {10.1016/j.scitotenv.2024.177519},
pmid = {39577582},
issn = {1879-1026},
mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Oxidative Stress/drug effects ; *Arsenic/toxicity ; *Kidney/drug effects ; *Fluorides/toxicity ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Chronic exposure to inorganic arsenic (iAs) and fluoride (F) affect gut health and potentially damage organs. The present study investigates the interplay between gut bacteria and oxidative stress (measured by MDA level, GSH level, catalase activity, Nrf2 translocation and expression) in zebrafish exposed to F (NaF 15 ppm) and As (As2O3 50 ppb) alone or in combination. Combined exposure to As and F reduced gut bacterial alteration and imposed less oxidative stress compared to F- exposure alone. V3-V4 metagenomic sequencing revealed Pseudomonas, Aeromonas and Plesiomonas genera dominated in As or F treated groups while As+F treated group was enriched in beneficial Lactococcus and Streptococcus genera. Functional KEGG analysis demonstrated treatment-specific changes in bacterial metabolism, host organismal systems, human diseases, as well as cellular processes of microbial community were significantly affected. When Aeromonas sp. isolated from F-treated fish gut, tagged with GFP-vector and fed (~3.2 × 10[6] CFU/mL) to untreated fish, induced oxidative stress in gut and kidney. Gut bacteria were found to both increase and mitigate iAs or F-toxicity, whereas As+F treatment promoted a protective response. Correlation analysis between gut microbial community at genus level and oxidative stress parameters of gut and kidney, showed Aeromonas and Plesiomonas genera are strongly correlated with oxidative stress (r = 0.5-0.9, p˂0.05). This study identifies microbiome biomarkers of iAs and F toxicity on gut-kidney axis.},
}

Animals
*Zebrafish
*Gastrointestinal Microbiome/drug effects
*Oxidative Stress/drug effects
*Arsenic/toxicity
*Kidney/drug effects
*Fluorides/toxicity
*Water Pollutants, Chemical/toxicity

@article {pmid39571816,
year = {2024},
author = {Arros, P and Palma, D and Gálvez-Silva, M and Gaete, A and Gonzalez, H and Carrasco, G and Coche, J and Perez, I and Castro-Nallar, E and Galbán, C and Varas, MA and Campos, M and Acuña, J and Jorquera, M and Chávez, FP and Cambiazo, V and Marcoleta, AE},
title = {Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177594},
doi = {10.1016/j.scitotenv.2024.177594},
pmid = {39571816},
issn = {1879-1026},
mesh = {*Soil Microbiology ; Antarctic Regions ; *Ice Cover/microbiology ; *Desert Climate ; *Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Biodiversity ; },
abstract = {The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Still, microbial life has been reported in these environments, with limited information on their genetic properties and functional capabilities. Although diverse autochthonous multidrug-resistant bacteria were found in Antarctic Peninsula soils, posing whether these soils could act as a source of resistance determinants that could emerge among pathogens, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a cold desert in West Antarctica. Despite the extreme conditions, several bacterial phyla were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. Contrastive with Ecology Glacier soils from King George Island, the Union Glacier soil bacterial community is significantly less diverse, mainly attributed to scarce moisture. We recovered >80 species-level representative genomes (SRGs) of predominant bacteria and an ammonia-oxidating nitrogen- and carbon-fixing archaeon from a novel species of Nitrosocosmicus. Several resistance and virulence genes were found in Union Glacier soils, similar to those in other Antarctic cold desert areas but significantly distinct from those observed in maritime Antarctica and other non-cryosphere biomes. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarctica's soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in this continent.},
}

*Soil Microbiology
Antarctic Regions
*Ice Cover/microbiology
*Desert Climate
*Bacteria/genetics
*Microbiota
Soil/chemistry
Biodiversity

@article {pmid39520912,
year = {2024},
author = {Zhao, L and Weng, W and Ni, M and Shen, H and Zhang, S and Chen, Y and Jia, R and Fan, L and Mao, Y and Qin, L and Liu, S and Wang, Y},
title = {Rubidium salt can effectively relieve the symptoms of DSS-induced ulcerative colitis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {181},
number = {},
pages = {117574},
doi = {10.1016/j.biopha.2024.117574},
pmid = {39520912},
issn = {1950-6007},
mesh = {*Colitis, Ulcerative/drug therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Dextran Sulfate ; Male ; Mice ; Mice, Inbred C57BL ; Salts ; Colon/drug effects/pathology/metabolism/microbiology ; Disease Models, Animal ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic condition that afflicts individuals repeatedly and cannot be cured at present, which has seriously affected the quality of life of patients. Minerals Containing Rubidium (MCR) from Guangxi Yuechengling, which Professor Zhao Lichun purified, were explored. Against this backdrop, the present study investigates the efficacy of rubidium salt in ulcerative colitis. Rubidium salt reduced levels of inflammatory markers and improved intestinal barrier function through the Elisa kit, immunohistochemistry, and qPCR. Next, we detected the level of short-chain fatty acid and found that the content of propanoic acid, butyric acid, and n-butyric acid increased after treatment with rubidium salt. We used fecal metagenomics to explore the underlying reasons further and found that rubidium salt significantly adjusted the structure of intestinal flora, increased the abundance of beneficial bacteria such as lactobacillus and bifidobacterium, and inhibited the abundance of harmful bacteria such as Enterobacteriaceae and Escherichia coli. We also learned that rubidium salt directly weakened pathogenic bacteria's infection and survival ability by reducing the expression of virulence factors such as fimH, invA, and hilA and virulence genes such as acrA and ompR. Overall, rubidium salt can reduce harmful bacteria and increase beneficial bacteria. The increased beneficial bacteria help enhance the gut barrier and regulate inflammatory factors by raising the levels of short-chain fatty acids. A strengthened gut barrier further stabilizes microbial homeostasis, ultimately alleviating ulcerative colitis.},
}

*Colitis, Ulcerative/drug therapy/microbiology
Animals
*Gastrointestinal Microbiome/drug effects
*Dextran Sulfate
Male
Mice
Mice, Inbred C57BL
Salts
Colon/drug effects/pathology/metabolism/microbiology
Disease Models, Animal

@article {pmid39515382,
year = {2024},
author = {Shan, E and Zhang, X and Yu, Z and Hou, C and Pang, L and Guo, S and Liu, Y and Dong, Z and Zhao, J and Wang, Q and Yuan, X},
title = {Seawater warming rather than acidification profoundly affects coastal geochemical cycling mediated by marine microbiome.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177365},
doi = {10.1016/j.scitotenv.2024.177365},
pmid = {39515382},
issn = {1879-1026},
mesh = {*Seawater/microbiology/chemistry ; *Microbiota ; *Climate Change ; Hydrogen-Ion Concentration ; Global Warming ; Denitrification ; Bacteria ; },
abstract = {The most concerning consequences of climate change include ocean acidification and warming, which can affect microbial communities and thus the biogeochemical cycling they mediate. Therefore, it is urgent to study the impact of ocean acidification and warming on microbial communities. In the current study, metagenomics was utilized to reveal how the structure and function of marine microorganisms respond to ocean warming and acidification. In terms of community structure, Non-metric Multidimensional Scaling analysis visualized the similarity or difference between the control and the warming or acidification treatments, but the inter-group differences were not significant. In terms of gene functionality, warming treatments showed greater effects on microbial communities than acidification. After treatment with warming, the relative abundance of genes associated with denitrification increased, suggesting that ocean nitrogen loss can increase with increased temperature. Conversely, acidification treatments apparently inhibited denitrification. Warming treatment also greatly affected sulfur-related microorganisms, increasing the relative abundance of certain sulfate-reducing prokaryote, and enriched microbial carbon-fixation pathways. These results provide information on the response strategies of coastal microorganisms in the changing marine environments.},
}

*Seawater/microbiology/chemistry
*Microbiota
*Climate Change
Hydrogen-Ion Concentration
Global Warming
Denitrification
Bacteria

@article {pmid38881311,
year = {2024},
author = {Blair, EM and Brown, JL and Li, D and Holden, PA and O'Malley, MA},
title = {Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential.},
journal = {Biotechnology progress},
volume = {40},
number = {6},
pages = {e3484},
doi = {10.1002/btpr.3484},
pmid = {38881311},
issn = {1520-6033},
support = {CNS-1725797//National Science Foundation/ ; //California NanoSystems Institute/ ; NSF DMR 2308708//Materials Research Laboratory, University of California, Santa Barbara, CA/ ; },
mesh = {*Metagenomics ; Animals ; Metagenome/genetics ; Anaerobiosis ; Feces/microbiology ; Goats ; Polymers/metabolism/chemistry ; Genome, Bacterial/genetics ; Bacteria, Anaerobic/genetics/metabolism/classification ; Microbial Consortia/genetics ; Biodegradation, Environmental ; Sewage/microbiology ; },
abstract = {Anaerobic microbial communities are often highly degradative, such as those found in the herbivore rumen and large-scale anaerobic digesters. Since the microbial communities in these systems degrade recalcitrant organic polymers, we hypothesize that some microbes in anaerobic environments may be involved in man-made plastic association, deformation, or even breakdown. While efforts have been put toward characterizing microbial communities, many microbes remain unidentified until they can be sufficiently cultivated to generate enough genetic material to assemble high-quality metagenome assemblies and reference genomes. In this study, microbial consortia from goat fecal pellets and anaerobic digester sludge were cultivated for over 6 weeks to assemble metagenomes from novel anaerobic taxa with potential degradative activity. To select for microbes with potential plastic-degrading abilities, plastic strips were included in culture, though the presence of plastic did not appear to enrich for particularly degradative consortia, yet it did select for novel species that otherwise may not have been characterized. Whole-genome shotgun sequencing enabled assembly of 72 prokaryotic metagenome-assembled genomes (MAGs) with >90% completion, <5% contamination, and an N50 >10,000 bp; 17 of these MAGs are classified as novel species given their lack of similarity to publicly available genomes and MAGs. These 72 MAGs vary in predicted carbohydrate-degrading abilities, with genes predicted to encode fewer than 10 or up to nearly 400 carbohydrate-active enzymes. Overall, this enrichment strategy enables characterization of less abundant MAGs in a community, and the MAGs identified here can be further mined to advance understanding of degradative anaerobic microbial consortia.},
}

*Metagenomics
Animals
Metagenome/genetics
Anaerobiosis
Feces/microbiology
Goats
Polymers/metabolism/chemistry
Genome, Bacterial/genetics
Bacteria, Anaerobic/genetics/metabolism/classification
Microbial Consortia/genetics
Biodegradation, Environmental
Sewage/microbiology

@article {pmid39701698,
year = {2024},
author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK},
title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {22},
pages = {5998-6007},
doi = {10.19540/j.cnki.cjcmm.20240508.401},
pmid = {39701698},
issn = {1001-5302},
mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.},
}

Animals
Mice
*Aging/drug effects
*Adipose Tissue/drug effects/metabolism
*Polysaccharides/pharmacology
*Indoles/pharmacology
Male
*Astragalus Plant/chemistry
3T3-L1 Cells
Humans
Adipocytes/drug effects/metabolism/cytology
Mice, Inbred C57BL
Cellular Senescence/drug effects
Drugs, Chinese Herbal/pharmacology/administration & dosage
Gastrointestinal Microbiome/drug effects

@article {pmid39696556,
year = {2024},
author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF},
title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {105},
pmid = {39696556},
issn = {2524-6372},
support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; },
abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.},
}

@article {pmid39695983,
year = {2024},
author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C},
title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {530},
pmid = {39695983},
issn = {1471-2180},
support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.},
}

Animals
*Equidae/microbiology
Cattle/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Tract/microbiology
Sequence Analysis, DNA/methods
Metagenome
Bacteroidetes/genetics/isolation & purification/classification

@article {pmid39695885,
year = {2024},
author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N},
title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {107},
pmid = {39695885},
issn = {2524-6372},
support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; },
abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.},
}

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {9},
number = {12},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation & purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation & purification ; },
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

*Anthozoa/virology/microbiology
Animals
*Microbiota/genetics
*Viruses/genetics/classification
*Metagenomics
Bacteria/genetics/classification/virology/isolation & purification
Symbiosis
Bacteriophages/genetics/physiology/classification/isolation & purification

@article {pmid39161223,
year = {2024},
author = {Stokholm, J and Thorsen, J and Schoos, AM and Rasmussen, MA and Brandt, S and Sørensen, SJ and Vahman, N and Chawes, B and Bønnelykke, K},
title = {Infantile colic is associated with development of later constipation and atopic disorders.},
journal = {Allergy},
volume = {79},
number = {12},
pages = {3360-3372},
doi = {10.1111/all.16274},
pmid = {39161223},
issn = {1398-9995},
support = {//Region Hovedstaden/ ; //Strategiske Forskningsråd/ ; //Lundbeck Foundation/ ; //Sundhed og Sygdom, Det Frie Forskningsråd/ ; },
mesh = {Humans ; *Constipation/epidemiology/etiology ; *Colic/epidemiology/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Infant ; Child, Preschool ; Dermatitis, Atopic/epidemiology/complications ; Child ; Prospective Studies ; Asthma/epidemiology/diagnosis/microbiology/etiology ; Hypersensitivity, Immediate/epidemiology/complications ; Risk Factors ; },
abstract = {BACKGROUND: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.

METHODS: Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.

RESULTS: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences.

CONCLUSIONS: We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.},
}

Humans
*Constipation/epidemiology/etiology
*Colic/epidemiology/etiology
*Gastrointestinal Microbiome
Male
Female
Infant
Child, Preschool
Dermatitis, Atopic/epidemiology/complications
Child
Prospective Studies
Asthma/epidemiology/diagnosis/microbiology/etiology
Hypersensitivity, Immediate/epidemiology/complications
Risk Factors

@article {pmid38742484,
year = {2024},
author = {Makri, N and Ring, N and Shaw, DJ and Athinodorou, A and Robinson, V and Paterson, GK and Richardson, J and Gow, D and Nuttall, T},
title = {Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals.},
journal = {Veterinary dermatology},
volume = {35},
number = {5},
pages = {479-491},
doi = {10.1111/vde.13256},
pmid = {38742484},
issn = {1365-3164},
support = {//R(D)SVS Hospital for Small Animals/ ; },
mesh = {Animals ; Rabbits/microbiology ; *Ear Canal/microbiology ; *Microbiota ; Female ; Male ; Otoscopy ; Bacteria/genetics/classification/isolation & purification ; Genomics ; Fungi/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking.

HYPOTHESIS/OBJECTIVES: This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing.

ANIMALS: Sixty-three otitis-free client-owned rabbits.

MATERIALS AND METHODS: All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed.

RESULTS: Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum.

Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.},
}

Animals
Rabbits/microbiology
*Ear Canal/microbiology
*Microbiota
Female
Male
Otoscopy
Bacteria/genetics/classification/isolation & purification
Genomics
Fungi/genetics/classification/isolation & purification

@article {pmid39695297,
year = {2024},
author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA},
title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1385},
pmid = {39695297},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; },
abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.},
}

Animals
Cattle/microbiology
*Feces/microbiology
*Metagenome
*Rumen/microbiology
*Phylogeny
Gastrointestinal Microbiome
Brazil
Male
Archaea/genetics/classification
Bacteria/genetics/classification
Microbiota

@article {pmid39695203,
year = {2024},
author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM},
title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1350},
pmid = {39695203},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; },
abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Archaea/genetics/classification
*Bacteria/genetics/classification
Arctic Regions
Microbiota
Oceans and Seas
Siberia

@article {pmid39693444,
year = {2024},
author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F},
title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.},
journal = {Science advances},
volume = {10},
number = {51},
pages = {eadq0645},
doi = {10.1126/sciadv.adq0645},
pmid = {39693444},
issn = {2375-2548},
mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; },
abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.},
}

*Microbiota/genetics
*Biodiversity
*Archaea/genetics/classification
*Phylogeny
*Bacteria/genetics/classification
Metagenome
Seawater/microbiology
Ecosystem

@article {pmid39637857,
year = {2024},
author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP},
title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.},
journal = {Cell reports. Medicine},
volume = {5},
number = {12},
pages = {101845},
doi = {10.1016/j.xcrm.2024.101845},
pmid = {39637857},
issn = {2666-3791},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Infant, Newborn ; Female ; Male ; *Infant, Premature ; Feces/microbiology ; Brain/pathology/microbiology ; Brain Diseases/microbiology/pathology ; Gestational Age ; Magnetic Resonance Imaging/methods ; Premature Birth/microbiology ; },
abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Infant, Newborn
Female
Male
*Infant, Premature
Feces/microbiology
Brain/pathology/microbiology
Brain Diseases/microbiology/pathology
Gestational Age
Magnetic Resonance Imaging/methods
Premature Birth/microbiology

@article {pmid39577267,
year = {2025},
author = {Ngo, C and Morrell, JM and Tummaruk, P},
title = {Boar semen microbiome: Insights and potential implications.},
journal = {Animal reproduction science},
volume = {272},
number = {},
pages = {107647},
doi = {10.1016/j.anireprosci.2024.107647},
pmid = {39577267},
issn = {1873-2232},
mesh = {Animals ; *Semen/microbiology ; Swine/microbiology/physiology ; Male ; *Microbiota ; Semen Analysis/veterinary ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.},
}

Animals
*Semen/microbiology
Swine/microbiology/physiology
Male
*Microbiota
Semen Analysis/veterinary
Bacteria/classification/isolation & purification/genetics

@article {pmid39565113,
year = {2024},
author = {Nowak, VV and Hou, P and Owen, JG},
title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {12},
pages = {e0072624},
doi = {10.1128/aem.00726-24},
pmid = {39565113},
issn = {1098-5336},
support = {Doctoral Scholarship//Victoria University of Wellington (WGTN)/ ; Contract 16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; RDF-VUW1601//Royal Society Te Apārangi (Royal Society of New Zealand)/ ; RTVU1908 and UOAX2010//Ministry for Business Innovation and Employment (MBIE)/ ; },
mesh = {*Porifera/microbiology ; Animals ; New Zealand ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenome ; *Microbiota ; Mediterranean Sea ; Multigene Family ; Metagenomics ; Phylogeny ; },
abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.},
}

*Porifera/microbiology
Animals
New Zealand
*Bacteria/genetics/classification/metabolism/isolation & purification
*Metagenome
*Microbiota
Mediterranean Sea
Multigene Family
Metagenomics
Phylogeny

@article {pmid39515242,
year = {2025},
author = {Wang, Y and Chen, S and Chen, Y and Xu, J and Zhou, J and He, Q and Lin, Z and Xu, KQ and Fan, G},
title = {Structure-activity relationship between crystal plane and pyrite-driven autotrophic denitrification efficacy: Electron transfer and metagenome-based microbial mechanism.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122756},
doi = {10.1016/j.watres.2024.122756},
pmid = {39515242},
issn = {1879-2448},
mesh = {*Denitrification ; Structure-Activity Relationship ; *Sulfides/chemistry/metabolism ; Nitrates/metabolism ; Water Purification ; *Electron Transport/genetics ; *Metagenome/genetics ; Bacteria/enzymology/genetics ; *Iron/chemistry/metabolism ; Electrochemistry ; Oxidation-Reduction ; *Microbiota ; },
abstract = {Pyrite-driven autotrophic denitrification (PAD) has been recognized as a promising treatment technology for nitrate removal. Although the occurrence of PAD has been found in recent years, there is a knowledge gap about effects of crystal plane of pyrite on the performance and mechanism of PAD system. Here, this study investigated the effects of crystal planes ({100},
{111}
and {210})
of single-crystal pyrite on denitrification performance, electron transfer, and microbial mechanism in PAD system. The removal efficiency of nitrate in B-{210}
reached 100%, which was 1.67-fold and 2.86-fold higher than that of B-{100}
and B-{111},
respectively. X-ray photoelectron spectroscopy and electrochemical results indicated that Fe-S bonds of pyrite with {210}
crystal plane were more susceptible to breakage by Fe[3+] oxidation assault, and leaching microbially available Fe[2+] and sulfur intermediates to drive autotrophic denitrification. Metagenomic results suggested that community of functional pyrite-driven denitrifiers varied in response to crystal plane, and abundances of N-S transformation and EET-related microbes and genes in B-{210}
notably up-regulated compared to B-{100}
and B-{111}.
In addition, this work proposed a dual-mode for electron transfer pathway during pyrite oxidation and nitrogen transformation in PAD system. In B-{210},
Fe(II)- and sulfur-driven denitrifiers obtained electron after pyrite oxidation-dissolution, and the enrichment of pyrite-oxidizing bacteria in B-{210}
could enhance the electron transfer from pyrite through electron shuttles. This work highlighted that stronger surface reactivity and electron shuttle effect in B-{210}
enhanced electron transfer, leading to favorable PAD performance in B-{210}.
Overall, this study provides novel insights into the structure-activity relationship between the crystal plane structure of pyrite and denitrification activity in PAD system.},
}

*Denitrification
Structure-Activity Relationship
*Sulfides/chemistry/metabolism
Nitrates/metabolism
Water Purification
*Electron Transport/genetics
*Metagenome/genetics
Bacteria/enzymology/genetics
*Iron/chemistry/metabolism
Electrochemistry
Oxidation-Reduction
*Microbiota

@article {pmid39503478,
year = {2024},
author = {Sun, H and Liu, X and Wang, T and Liu, S and Zhang, R and Guo, X and Yu, Z and Zhao, Y and Shen, P and Zhang, Y},
title = {Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {12},
pages = {e0175424},
doi = {10.1128/aem.01754-24},
pmid = {39503478},
issn = {1098-5336},
support = {U2106208//NSFC-Shandong Joint Fund/ ; 41976147//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Rhizosphere ; *Microbiota ; *Zosteraceae/microbiology ; China ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; Alismatales/microbiology ; Metagenome ; },
abstract = {UNLABELLED: Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE: Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.},
}

*Rhizosphere
*Microbiota
*Zosteraceae/microbiology
China
Bacteria/classification/genetics/isolation & purification/metabolism
Soil Microbiology
Alismatales/microbiology
Metagenome

@article {pmid39215755,
year = {2024},
author = {Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Giuliani, F and Riva, M and Ungaro, F and Guerra, M and Brina, ALD and Biscaglia, G and Tavano, F and Carparelli, S and Fiorino, G and Danese, S and Perri, F and Palmieri, O},
title = {Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.},
journal = {United European gastroenterology journal},
volume = {12},
number = {10},
pages = {1461-1480},
doi = {10.1002/ueg2.12655},
pmid = {39215755},
issn = {2050-6414},
support = {PNRR-MAD-2022-12375729//Italian Next Generation Eu Program/ ; },
mesh = {Humans ; *Artificial Intelligence ; *Proteomics/methods ; *Metagenomics/methods ; *Genomics/methods ; *Inflammatory Bowel Diseases/microbiology/genetics ; Precision Medicine/methods ; Transcriptome ; Crohn Disease/microbiology/genetics/immunology ; Gastrointestinal Microbiome/immunology ; Colitis, Ulcerative/microbiology/genetics/immunology ; },
abstract = {Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.},
}

Humans
*Artificial Intelligence
*Proteomics/methods
*Metagenomics/methods
*Genomics/methods
*Inflammatory Bowel Diseases/microbiology/genetics
Precision Medicine/methods
Transcriptome
Crohn Disease/microbiology/genetics/immunology
Gastrointestinal Microbiome/immunology
Colitis, Ulcerative/microbiology/genetics/immunology

@article {pmid38309691,
year = {2025},
author = {Yuan, Q and Liu, W and Hao, W and Chen, Y and Xiao, Y and Li, H and Shui, M and Wu, DT and Wang, S},
title = {Glycosidic linkages of fungus polysaccharides influence the anti-inflammatory activity in mice.},
journal = {Journal of advanced research},
volume = {67},
number = {},
pages = {161-172},
doi = {10.1016/j.jare.2024.01.037},
pmid = {38309691},
issn = {2090-1224},
mesh = {Animals ; Mice ; *Anti-Inflammatory Agents/pharmacology/chemistry ; *Colitis/drug therapy/metabolism/chemically induced ; *Dextran Sulfate ; *Fungal Polysaccharides/chemistry/pharmacology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Glycosides/pharmacology/chemistry ; Male ; Mice, Inbred C57BL ; Basidiomycota/chemistry ; Polysaccharides/chemistry/pharmacology ; Cytokines/metabolism ; },
abstract = {INTRODUCTION: Over decades, the source-function relationships of bioactive polysaccharides have been progressively investigated, however, it is still unclear how a defined structure may conduce to the bioactivities of polysaccharides.

OBJECTIVES: To explore the structure-function relationship of fungus polysaccharides, we employed a dextran sulfate sodium (DSS)-induced colitis mouse model to compare the anti-inflammatory activity of two fungus polysaccharides from Dictyophora indusiata (DIP) and Tremella fuciformis (TFP), which exhibit distinct glycosidic linkages.

METHODS: The structures of DIP and TFP were characterized through molecular weight detection, molecular morphology analysis, methylation analysis, and NMR analysis. Subsequently, we employed a DSS-induced colitis model to assess the anti-inflammatory efficacy of DIP and TFP. The colitis symptoms, histological morphology, intestinal inflammatory cytokines, and the composition and function of gut microbiota before and after polysaccharides treatment in colitis mice were also investigated.

RESULTS: DIP, l,3-β-D-glucan with 1,4-β and 1,6-β-D-Glcp as branched chains, exhibited superior therapeutic effect than that of TFP consisted of a linear 1,3-α-D-mannose backbone with D-xylose and L-fucose in the side chains. Both DIP and TFP relieved DSS-induced colitis in a gut microbiota-dependent manner. Furthermore, metagenomics showed that DIP and TFP could partially reverse the bacterial function in colitis mice. Glycoside Hydrolase 1 (GH1) and GH3 were identified as being involved in hydrolyzing the glucose linkages in DIP, while GH92 and GH29 were predicted to be active in cleaving the α-1,3-linked mannose linkages and the glycosidic bonds of L-fucose residues in TFP.

CONCLUSION: Our findings highlight the pivotal role of glycosidic linkages in anti-inflammatory activities of fungus polysaccharides and would promote the design and discovery of polysaccharides with designated activity to be used as functional foods and/or therapeutics.},
}

Animals
Mice
*Anti-Inflammatory Agents/pharmacology/chemistry
*Colitis/drug therapy/metabolism/chemically induced
*Dextran Sulfate
*Fungal Polysaccharides/chemistry/pharmacology
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Glycosides/pharmacology/chemistry
Male
Mice, Inbred C57BL
Basidiomycota/chemistry
Polysaccharides/chemistry/pharmacology
Cytokines/metabolism

@article {pmid39684893,
year = {2024},
author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE},
title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313183},
pmid = {39684893},
issn = {1422-0067},
support = {C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; },
abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.},
}

Animals
Male
Female
*Anxiety/metabolism
Rats
*Loperamide/pharmacology
*Brain/metabolism/drug effects
*Rats, Sprague-Dawley
*Receptors, Opioid/metabolism/genetics
Behavior, Animal/drug effects
Gastrointestinal Microbiome/drug effects
Hippocampus/metabolism/drug effects
Enteric Nervous System/metabolism
Gene Expression Regulation/drug effects
Sex Factors
Sex Characteristics

@article {pmid39684853,
year = {2024},
author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK},
title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313143},
pmid = {39684853},
issn = {1422-0067},
support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; },
abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Dental Enamel Hypoplasia/microbiology/genetics
Child
Mouth Mucosa/microbiology/pathology
Male
Female
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Metagenome
Incisor/microbiology
Molar Hypomineralization

@article {pmid39684458,
year = {2024},
author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S},
title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312747},
pmid = {39684458},
issn = {1422-0067},
support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; },
mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; },
abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.},
}

*Microbial Consortia
*Wastewater/microbiology
*Biodegradation, Environmental
Sewage/microbiology
Plastics/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Microbiota

@article {pmid39684246,
year = {2024},
author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M},
title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312534},
pmid = {39684246},
issn = {1422-0067},
support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; },
mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; },
abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.},
}

Animals
Female
Male
*Feces/microbiology
Mice
*Gastrointestinal Microbiome/drug effects
*Toll-Like Receptor 4/genetics/metabolism
*Metagenomics/methods
*Mice, Knockout
*RNA, Ribosomal, 16S/genetics
*Ethanol/adverse effects
Alcohol Drinking/adverse effects
Mice, Inbred C57BL
Sex Factors
Dysbiosis/microbiology/chemically induced
Sex Characteristics

@article {pmid39683635,
year = {2024},
author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T},
title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
doi = {10.3390/nu16234242},
pmid = {39683635},
issn = {2072-6643},
support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; },
abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.},
}

Humans
Burkina Faso
Female
Infant, Newborn
*Gastrointestinal Microbiome
*Milk, Human/immunology
Prospective Studies
*Vagina/microbiology/immunology
*Immune System
Pregnancy
Breast Feeding
Infant, Small for Gestational Age
Adult

@article {pmid39682735,
year = {2024},
author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M},
title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
doi = {10.3390/cells13231987},
pmid = {39682735},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; },
abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/microbiology
Machine Learning
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods

@article {pmid39681310,
year = {2024},
author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME},
title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100434},
doi = {10.1016/j.jfp.2024.100434},
pmid = {39681310},
issn = {1944-9097},
abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1× PBS or 1× PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.},
}

@article {pmid39630952,
year = {2024},
author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA},
title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.},
journal = {Environmental science & technology},
volume = {58},
number = {50},
pages = {22053-22063},
doi = {10.1021/acs.est.4c09642},
pmid = {39630952},
issn = {1520-5851},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Child ; *Metals ; Prospective Studies ; Female ; Male ; Birth Cohort ; Environmental Exposure ; Multiomics ; },
abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.},
}

Humans
*Gastrointestinal Microbiome
*Feces/microbiology
Child
*Metals
Prospective Studies
Female
Male
Birth Cohort
Environmental Exposure
Multiomics

@article {pmid39601556,
year = {2024},
author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P},
title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0136624},
doi = {10.1128/msystems.01366-24},
pmid = {39601556},
issn = {2379-5077},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology ; Mice ; *Ethanol ; Male ; Mice, Inbred C57BL ; Metagenome/drug effects ; Liver/metabolism/drug effects/pathology ; Sexual Maturation/drug effects ; },
abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.

IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced/microbiology
Mice
*Ethanol
Male
Mice, Inbred C57BL
Metagenome/drug effects
Liver/metabolism/drug effects/pathology
Sexual Maturation/drug effects

@article {pmid39601555,
year = {2024},
author = {Gao, Y and Zhang, H and Zhu, D and Guo, L},
title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0095424},
doi = {10.1128/msystems.00954-24},
pmid = {39601555},
issn = {2379-5077},
support = {561119219//Scientific research start-up foundation from Lanzhou University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Otters/microbiology ; *Feces/microbiology ; *Animal Feed/analysis/microbiology ; Animals, Zoo/microbiology ; Diet/veterinary ; Bacteria/genetics/isolation & purification/classification ; Fatty Acids, Volatile/metabolism ; },
abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.

IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.},
}

Animals
*Gastrointestinal Microbiome
*Otters/microbiology
*Feces/microbiology
*Animal Feed/analysis/microbiology
Animals, Zoo/microbiology
Diet/veterinary
Bacteria/genetics/isolation & purification/classification
Fatty Acids, Volatile/metabolism

@article {pmid39584840,
year = {2024},
author = {Bernardin, JR and Young, EB and Gray, SM and Bittleston, LS},
title = {Bacterial community function increases leaf growth in a pitcher plant experimental system.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0129824},
doi = {10.1128/msystems.01298-24},
pmid = {39584840},
issn = {2379-5077},
mesh = {*Plant Leaves/microbiology/growth & development ; *Sarraceniaceae/microbiology ; *Microbiota/physiology ; *Bacteria/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.

IMPORTANCE: This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.},
}

*Plant Leaves/microbiology/growth & development
*Sarraceniaceae/microbiology
*Microbiota/physiology
*Bacteria/genetics
Metagenomics

@article {pmid39557257,
year = {2024},
author = {Dong, J and Wang, L and Bai, Y and Huang, X and Chen, C and Liu, Y},
title = {Study on the physicochemical properties and immune regulatory mechanism of polysaccharide fraction from Aronia Melanocarpa fruit.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 2},
pages = {137696},
doi = {10.1016/j.ijbiomac.2024.137696},
pmid = {39557257},
issn = {1879-0003},
mesh = {*Photinia/chemistry ; *Polysaccharides/pharmacology/chemistry ; Animals ; Mice ; *Fruit/chemistry ; *Gastrointestinal Microbiome/drug effects ; Chemical Phenomena ; Molecular Weight ; },
abstract = {Aronia Melanocarpa (Michx.) Elliott fruit has been extensively used in the food and medicinal fields. This study aimed to analyze the physicochemical properties of a polysaccharide fraction (AMP2) isolated from this fruit for the first time and investigated its immune regulatory mechanism. The physicochemical properties of AMP2 were determined using high-performance gel permeation chromatography, PMP derivatization-high performance liquid chromatography, Ultraviolet spectroscopy, and infrared spectroscopy. The metagenomic technology was applied to investigate the regulatory effects and mechanisms of AMP2 on the gut microbiota of immunosuppressed mice. The results showed that molecular weight of AMP2 was 83,444 Da, which was mainly composed of D-arabinose, D-xylose, D-mannose, D-rhamnose and D-glucose, and both β-type and α-type glycosidic bonds contained in its structure. AMP2 changed the composition of gut microbiota by increasing the number of beneficial and probiotic bacteria, thereby regulated the intestinal mucosal immune system of host. AMP2 improved intestinal immune system response and antimicrobial capacity through positive regulation of the NOD-like receptor signaling pathway and neutrophil extracellular trap formation. The results demonstrate the potential of AMP2 in immune regulation, providing a new perspective for its subsequent development and contributing to the development and application of related health foods.},
}

*Photinia/chemistry
*Polysaccharides/pharmacology/chemistry
Animals
Mice
*Fruit/chemistry
*Gastrointestinal Microbiome/drug effects
Chemical Phenomena
Molecular Weight

@article {pmid39557245,
year = {2024},
author = {Qin, X and Huang, W and Li, Q},
title = {Lignocellulose biodegradation to humic substances in cow manure-straw composting: Characterization of dissolved organic matter and microbial community succession.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 3},
pages = {137758},
doi = {10.1016/j.ijbiomac.2024.137758},
pmid = {39557245},
issn = {1879-0003},
mesh = {*Humic Substances/analysis ; *Lignin/chemistry/metabolism ; *Manure/microbiology/analysis ; Cattle ; Animals ; *Composting/methods ; *Biodegradation, Environmental ; Microbiota ; },
abstract = {Composting, a sustainable practice, facilitates the biodegradation of organic waste, notably lignocellulosic biomass, into value-added humic substances. Despite its potential, the application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to characterize dissolved organic matter (DOM) for assessing the changes in maturity during cow manure-straw composting is underexplored. Furthermore, the link between these changes, microbial community succession, and the biochemical pathways of humus formation is seldom investigated. This study leveraged ESI FT-ICR MS and metagenomic analysis to elucidate the molecular changes in DOM, identified key microbes in humus formation, and traced the humus formation pathway during composting. The results highlighted the crucial role of microorganisms such as Thermobifida, Luteimonas, Ascomycota, and Chloroflexi in accelerating the breakdown and transformation of plant biopolymers. Large molecular nitrogen compounds from cow manure-straw were converted into unsaturated, aromatic oxygen compounds, which resemble humic substances in their chemical properties. The ESI FT-ICR MS data revealed that humus formation occurred through a series of reactions, including protein deamination, lignin delignification, and decarbonylation. This research offered new light on strategies to enhance the stabilization and humification of cow manure-straw composting, contributing to more effective composting processes.},
}

*Humic Substances/analysis
*Lignin/chemistry/metabolism
*Manure/microbiology/analysis
Cattle
Animals
*Composting/methods
*Biodegradation, Environmental
Microbiota

@article {pmid39551294,
year = {2024},
author = {Zhang, G and Du, J and Zhang, C and Zhao, Z and Chen, Y and Liu, M and Chen, J and Fan, G and Ma, L and Li, S and Liu, K},
title = {Identification of a PET hydrolytic enzyme from the human gut microbiome unveils potential plastic biodegradation in human digestive tract.},
journal = {International journal of biological macromolecules},
volume = {283},
number = {Pt 3},
pages = {137732},
doi = {10.1016/j.ijbiomac.2024.137732},
pmid = {39551294},
issn = {1879-0003},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Polyethylene Terephthalates/metabolism/chemistry ; *Biodegradation, Environmental ; Hydrolysis ; Gastrointestinal Tract/microbiology/metabolism ; Metagenome ; Hydrolases/metabolism/genetics ; Plastics/chemistry ; Nanoparticles/chemistry ; },
abstract = {Widespread use of polyethylene terephthalate (PET) plastics and their recycling challenges have led to substantial accumulation of PET wastes in global environments, with inevitable consequences for their entry into the food chains. Recent studies have increasingly documented the ingestion of microplastics by humans through food and beverages. However, the fate of these microplastics within the gastrointestinal tract, particularly the role of the human gut microbiota, remains inadequately understood. To address this knowledge gap, we employed a bioinformatics workflow integrated with functional verification to investigate the PET digestion/degradation capabilities of intestinal microorganisms. This approach identified a novel PET hydrolase-HGMP01 from the human gut metagenome, which exhibits the capacity to hydrolyze PET nanoparticles. Moreover, comprehensive exploration for HGMP01 homologues in the human gut metagenome and metatranscriptome unveil their distribution in diverse intestinal microorganisms. This study provides biochemical evidence for an unforeseen role of human gut microbiome in plastic digestion, thus holding substantial implications for human health.},
}

Humans
*Gastrointestinal Microbiome
*Polyethylene Terephthalates/metabolism/chemistry
*Biodegradation, Environmental
Hydrolysis
Gastrointestinal Tract/microbiology/metabolism
Metagenome
Hydrolases/metabolism/genetics
Plastics/chemistry
Nanoparticles/chemistry

@article {pmid39508593,
year = {2024},
author = {Tran, TH and F Escapa, I and Roberts, AQ and Gao, W and Obawemimo, AC and Segre, JA and Kong, HH and Conlan, S and Kelly, MS and Lemon, KP},
title = {Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.},
journal = {mSystems},
volume = {9},
number = {12},
pages = {e0113224},
doi = {10.1128/msystems.01132-24},
pmid = {39508593},
issn = {2379-5077},
support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; R35 GM141806/GM/NIGMS NIH HHS/United States ; R35 GM141806, R01 GM117174//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; K23 AI135090/AI/NIAID NIH HHS/United States ; //HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; //HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; FPILOT45//Forsyth Institute/ ; },
mesh = {*Corynebacterium/genetics/metabolism ; Humans ; *Genome, Bacterial ; *Phylogeny ; Microbiota/genetics ; Genomics ; United States ; Nose/microbiology ; Botswana ; },
abstract = {UNLABELLED: Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE: Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.},
}

*Corynebacterium/genetics/metabolism
Humans
*Genome, Bacterial
*Phylogeny
Microbiota/genetics
Genomics
United States
Nose/microbiology
Botswana

@article {pmid39316987,
year = {2024},
author = {Yang, H and Liu, Y and Cao, G and Liu, J and Xiao, S and Xiao, P and Tao, Y and Gao, H},
title = {Effects of lycopene on the growth performance, meat quality, cecal metagenome, and hepatic untargeted metabolome in heat stressed broilers.},
journal = {Poultry science},
volume = {103},
number = {12},
pages = {104299},
pmid = {39316987},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/growth & development ; *Animal Feed/analysis ; *Diet/veterinary ; *Meat/analysis ; *Liver/drug effects/metabolism ; *Lycopene/pharmacology/administration & dosage ; *Cecum/microbiology/drug effects/metabolism ; *Dietary Supplements/analysis ; *Metabolome/drug effects ; Male ; Metagenome ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; Heat-Shock Response/drug effects ; },
abstract = {The occurrence of heat stress in poultry houses is inevitable and leads to oxidative stress in the birds. Lycopene, a natural hydrocarbon carotenoid, possesses potent antioxidant properties. This study aimed to investigate the impact of lycopene on growth performance, meat quality, cecal microflora, and liver metabolome in broilers subjected to heat stress. A total of 480 yellow feather broilers were randomly allocated into 4 treatment groups: birds fed standard diet (Con), birds fed standard diet and supplemented with lycopene (Lyc), birds fed standard diet and subjected to heat stress (Hs), and birds fed with lycopene and subjected to heat stress (Hs-Lyc). As compared with the normal temperature groups, Hs decreased the average daily gain (ADG) of birds during d 1 to 28, lowered the pH value either in breast meat or thigh meat, increased the L* value of breast meat, and decreased the a* value of thigh meat. In comparison with non-Lyc feeding birds, Lyc supplement elevated the ADG during d 1 to 56, increased the pH of breast meat, decrease the L* and b* values of thigh meat, simultaneously increase the a* value of thigh meat. The L* of breast meat and pH of thigh meat exhibited significant differences under Hs-Lyc treatment. Lyc-treated birds exhibited higher elasticity, gumminess, and resilience in breast meat than those in non-Lyc feeding birds. The cecal metagenome analysis indicated that Hs-Lyc treatment increased the abundance of Phocaeicola salanitronis and Prevotella sp.CAG:1058, Bacteroides sp.An269, and Bacteroides sp.An19 at the species level compared with other treatments. The hepatic untargeted metabolome analysis showed that administration of Lyc upregulated 20 metabolites and downregulated 60 metabolites compared to the Con birds. Futhermore, the Hs-Lyc treatment upregulated 34 metabolites and downregulated 45 metabolites compared to the Hs birds. The correlation between the metagenome and metabolome showed that Lyc supplementation induced significant alterations in the citrate cycle, metabolism of butanoate, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate, alanine, aspartate, and glutamate compared with standard supplement. In contrast, Hs-Lyc treatment induced alterations in the citrate cycle, metabolism of pyruvate, glyoxylate, and dicarboxylate, glycolysis/gluconeogenesis, arginine, proline, alanine, aspartate, and glutamate compared with the standard supplement of heat-challenged broilers. In summary, dietary Lyc supplementation promoted the growth performance, changed the meat quality, modulated the cecal metagenome and hepatic metabolome in heat-stressed broilers.},
}

Animals
*Chickens/physiology/growth & development
*Animal Feed/analysis
*Diet/veterinary
*Meat/analysis
*Liver/drug effects/metabolism
*Lycopene/pharmacology/administration & dosage
*Cecum/microbiology/drug effects/metabolism
*Dietary Supplements/analysis
*Metabolome/drug effects
Male
Metagenome
Random Allocation
Gastrointestinal Microbiome/drug effects
Heat-Shock Response/drug effects

@article {pmid39679737,
year = {2024},
author = {Zhao, H and Wang, T},
title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.},
journal = {Biometrics},
volume = {80},
number = {4},
pages = {},
doi = {10.1093/biomtc/ujae153},
pmid = {39679737},
issn = {1541-0420},
mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; },
abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.},
}

Humans
Calibration
*Models, Statistical
Gastrointestinal Microbiome
Computer Simulation
Regression Analysis
Bias
Linear Models
Biometry/methods
Data Interpretation, Statistical
Metagenomics/methods/statistics & numerical data

@article {pmid39679619,
year = {2024},
author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K},
title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2405547},
doi = {10.1080/19490976.2024.2405547},
pmid = {39679619},
issn = {1949-0984},
mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; },
abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.},
}

Humans
*Obesity/microbiology
*Feces/microbiology
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Adult
*Duodenum/microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
Jejunum/microbiology
Mouth/microbiology
Nutritional Status

@article {pmid39679617,
year = {2024},
author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC},
title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2385524},
doi = {10.1080/19490976.2024.2385524},
pmid = {39679617},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; },
abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.},
}

*Gastrointestinal Microbiome
Animals
Mice
Male
*Autism Spectrum Disorder/microbiology
*Body Weight
Female
*Behavior, Animal
Disease Models, Animal
Humans
Brain-Gut Axis/physiology
Bacteria/classification/isolation & purification/genetics
Autistic Disorder/microbiology/psychology

@article {pmid39679616,
year = {2024},
author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D},
title = {Gut microbiota genome features associated with brain injury in extremely premature infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410479},
doi = {10.1080/19490976.2024.2410479},
pmid = {39679616},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; },
abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Infant, Extremely Premature
*Brain Injuries/microbiology/genetics
*Feces/microbiology
Female
Male
Bacteria/genetics/classification/isolation & purification/metabolism
Genome, Bacterial
Cohort Studies

@article {pmid39678952,
year = {2024},
author = {Sinha, T and Talukdar, NC},
title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.},
journal = {Indian journal of microbiology},
volume = {64},
number = {4},
pages = {1587-1597},
pmid = {39678952},
issn = {0046-8991},
abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.},
}

@article {pmid39676101,
year = {2024},
author = {Wang, C and Zhang, C and He, S and Wang, Q and Gao, H},
title = {The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis.},
journal = {Progress in orthodontics},
volume = {25},
number = {1},
pages = {48},
pmid = {39676101},
issn = {2196-1042},
support = {PY2023038//Science research cultivation program of stomatological hospital, Southern medical university/ ; PY2023043//Science research cultivation program of stomatological hospital, Southern medical university/ ; B2023274//Guangdong Medical Research Fund/ ; B2022013//Guangdong Medical Research Fund/ ; },
mesh = {Humans ; Adolescent ; *Dental Plaque/microbiology ; Male ; *Microbiota ; Female ; *Biofilms ; Child ; *Capnocytophaga ; Neisseria ; Metagenomics/methods ; Virulence Factors/genetics ; },
abstract = {BACKGROUND: White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.

METHODS: Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.

RESULTS: A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.

CONCLUSION: In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.},
}

Humans
Adolescent
*Dental Plaque/microbiology
Male
*Microbiota
Female
*Biofilms
Child
*Capnocytophaga
Neisseria
Metagenomics/methods
Virulence Factors/genetics

@article {pmid39434565,
year = {2025},
author = {Blattner, LA and Lapellegerie, P and Courtney-Mustaphi, C and Heiri, O},
title = {Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14035},
pmid = {39434565},
issn = {1755-0998},
mesh = {Animals ; *Chironomidae/genetics/classification ; *Lakes ; *DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/chemistry ; *Biodiversity ; Switzerland ; Larva/genetics/classification ; DNA/genetics/chemistry ; Chitin ; Metagenomics/methods ; },
abstract = {Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets.},
}

Animals
*Chironomidae/genetics/classification
*Lakes
*DNA Barcoding, Taxonomic/methods
*Geologic Sediments/chemistry
*Biodiversity
Switzerland
Larva/genetics/classification
DNA/genetics/chemistry
Chitin
Metagenomics/methods

@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; },
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}

*Neuromyelitis Optica/microbiology/immunology
Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology
Animals
Female
Adult
*Fecal Microbiota Transplantation
Mice
Male
Metabolome/physiology
Middle Aged

@article {pmid39010331,
year = {2025},
author = {Aydin, Ö and Wahlström, A and de Jonge, PA and Meijnikman, AS and Sjöland, W and Olsson, L and Henricsson, M and de Goffau, MC and Oonk, S and Bruin, SC and Acherman, YIZ and Marschall, HU and Gerdes, VEA and Nieuwdorp, M and Bäckhed, F and Groen, AK},
title = {An integrated analysis of bile acid metabolism in humans with severe obesity.},
journal = {Hepatology (Baltimore, Md.)},
volume = {81},
number = {1},
pages = {19-31},
doi = {10.1097/HEP.0000000000000938},
pmid = {39010331},
issn = {1527-3350},
mesh = {Humans ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; *Feces/microbiology/chemistry ; *Obesity, Morbid/metabolism/microbiology ; Fibroblast Growth Factors/metabolism ; },
abstract = {BACKGROUND AND AIMS: Bile acids (BA) are vital regulators of metabolism. BAs are AQ6 secreted in the small intestine, reabsorbed, and transported back to the liver, where they can modulate metabolic functions. There is a paucity of data regarding the portal BA composition in humans. This study aimed to address this knowledge gap by investigating portal BA composition and the relation with peripheral and fecal BA dynamics in conjunction with the gut microbiome.

APPROACH AND RESULTS: Thirty-three individuals from the BARIA cohort were included. Portal plasma, peripheral plasma, and feces were collected. BA and C4 levels were measured employing mass spectrometry. FGF19 was measured using ELISA. Gut microbiota composition was determined through metagenomics analysis on stool samples. Considerable diversity in the portal BA composition was observed. The majority (n = 26) of individuals had a 9-fold higher portal than peripheral BA concentration. In contrast, 8 individuals showed lower portal BA concentration compared with peripheral and had higher levels of unconjugated and secondary BA in this compartment, suggesting more distal origin. The altered portal BA profile was associated with altered gut microbiota composition. In particular, taxa within Bacteroides were reduced in abundance in the feces of these individuals.

CONCLUSIONS: Characterization of the portal BA composition in relation to peripheral and fecal BA increased insight into the dynamics of BA metabolism in individuals with obesity. Peripheral BA composition was much more diverse due to microbial metabolism. About 24% of the portal samples was surprisingly low in total BA; the underlying mechanism requires further exploration.},
}

Humans
*Bile Acids and Salts/metabolism
Male
Female
*Gastrointestinal Microbiome/physiology
Adult
Middle Aged
*Feces/microbiology/chemistry
*Obesity, Morbid/metabolism/microbiology
Fibroblast Growth Factors/metabolism

@article {pmid39674265,
year = {2024},
author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B},
title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbae646},
pmid = {39674265},
issn = {1477-4054},
support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; },
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; },
abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Sequence Analysis, DNA/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome
Workflow
DNA Contamination

@article {pmid39669269,
year = {2024},
author = {Lee, KH and Kim, YO and Dho, SH and Yong, JJH and Oh, HS and Lee, JH and Yang, SJ and Cha, I and Chun, J and Lee, EH and Jeong, SJ and Woo, W and Choi, JP and Han, SH and Choi, GB and Huh, JR and Kim, LK and Song, YG},
title = {Altered gut microbiome in convalescent patients with coronavirus disease 2019.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1455295},
pmid = {39669269},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology/virology ; Middle Aged ; Prospective Studies ; *SARS-CoV-2/isolation & purification ; Longitudinal Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Convalescence ; Bacteria/classification/isolation & purification/genetics ; Aged ; },
abstract = {INTRODUCTION: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.

METHODS: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls. Differences in the gut microbiota were analysed using 16S ribosomal RNA sequencing. The first stool samples were collected at an early convalescent phase of COVID-19, and the second sample was collected at least seven months after COVID-19 infection.

RESULTS AND DISCUSSION: At the order level, Eubacteriales and Bifidobacteriales decreased, while Bacteroidales and Burkholderiales increased in the COVID-19 group compared to the controls. Alpha diversity also decreased in COVID-19 patients compared to controls, with imperfect recovery of the gut microbiome after seven months. The compositional change in the gut microbiome between the early and late convalescent phases was largest in the moderate and severe groups. The severity of COVID-19 was the most influential clinical variable for microbiome composition (Sum of Sqs = 0.686, P = 0.006), and its effect persisted even after partialling out other effects such as antibiotic use and age. Thus, our study indicates a possible interaction between respiratory viral infection and the composition of the gut microbiota community, warranting future mechanistic and prospective longitudinal studies. Additionally, we were able to detect microbiome changes in patients who were re-infected with SARS-CoV-2. Notably, the dominant bacteria in the re-infected group were Lachnospiraceae and Faecalimonas umbilicata, compared to the one-time infected group.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
Male
Female
*Feces/microbiology/virology
Middle Aged
Prospective Studies
*SARS-CoV-2/isolation & purification
Longitudinal Studies
*RNA, Ribosomal, 16S/genetics
Adult
Severity of Illness Index
Convalescence
Bacteria/classification/isolation & purification/genetics
Aged

@article {pmid39551110,
year = {2025},
author = {Adenaike, AS and Akpan, U and Oyedun, IO and Adewole, FA and Agbaje, M and Olusanya, OM and Arowosegbe, MO and Ikeobi, CON},
title = {Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment.},
journal = {Microbial pathogenesis},
volume = {198},
number = {},
pages = {107126},
doi = {10.1016/j.micpath.2024.107126},
pmid = {39551110},
issn = {1096-1208},
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Genotype ; *Tropical Climate ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Feathers/microbiology ; Bacteroidetes/genetics/isolation & purification/classification ; Phylogeny ; Firmicutes/genetics/isolation & purification/classification ; Actinobacteria/genetics/classification/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers' health.},
}

Animals
*Chickens/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Genotype
*Tropical Climate
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Feathers/microbiology
Bacteroidetes/genetics/isolation & purification/classification
Phylogeny
Firmicutes/genetics/isolation & purification/classification
Actinobacteria/genetics/classification/isolation & purification
Biodiversity
DNA, Bacterial/genetics
Gastrointestinal Tract/microbiology

@article {pmid39367251,
year = {2024},
author = {Zheng, J and Sun, Q and Zhang, M and Liu, C and Su, Q and Zhang, L and Xu, Z and Lu, W and Ching, J and Tang, W and Cheung, CP and Hamilton, AL and Wilson O'Brien, AL and Wei, SC and Bernstein, CN and Rubin, DT and Chang, EB and Morrison, M and Kamm, MA and Chan, FKL and Zhang, J and Ng, SC},
title = {Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.},
journal = {Nature medicine},
volume = {30},
number = {12},
pages = {3555-3567},
pmid = {39367251},
issn = {1546-170X},
support = {R4030-22//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 14121322//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017PG-IBD003//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; 10210816//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 82100573//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; *Crohn Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Biomarkers ; *Colitis, Ulcerative/microbiology/diagnosis ; Female ; Male ; Adult ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Bacteria/genetics/isolation & purification ; Metagenomics/methods ; Middle Aged ; Case-Control Studies ; Microbiota/genetics ; },
abstract = {Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.},
}

Humans
*Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/diagnosis
*Crohn Disease/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
*Biomarkers
*Colitis, Ulcerative/microbiology/diagnosis
Female
Male
Adult
Leukocyte L1 Antigen Complex/analysis/metabolism
Bacteria/genetics/isolation & purification
Metagenomics/methods
Middle Aged
Case-Control Studies
Microbiota/genetics

@article {pmid39591974,
year = {2024},
author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM},
title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.},
journal = {Cell host & microbe},
volume = {32},
number = {12},
pages = {2212-2230.e8},
doi = {10.1016/j.chom.2024.10.017},
pmid = {39591974},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; Infant ; Humans ; *Virome/genetics ; *Metagenome/genetics ; Child, Preschool ; Infant, Newborn ; Child ; Bacteriophages/genetics/isolation & purification ; Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; Feces/microbiology/virology ; Metagenomics/methods ; Female ; Bifidobacterium/genetics/isolation & purification/classification ; Phylogeny ; Male ; Genome, Bacterial ; },
abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.},
}

*Gastrointestinal Microbiome/genetics
Infant
Humans
*Virome/genetics
*Metagenome/genetics
Child, Preschool
Infant, Newborn
Child
Bacteriophages/genetics/isolation & purification
Bacteria/genetics/virology/classification
Genome, Viral/genetics
Feces/microbiology/virology
Metagenomics/methods
Female
Bifidobacterium/genetics/isolation & purification/classification
Phylogeny
Male
Genome, Bacterial

@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {12},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; },
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.},
}

*Soil Microbiology
*Bacteria/genetics/classification
*Archaea/genetics/classification
*Microbiota
*Salinity
*Fungi/genetics/classification
Climate Change
Desert Climate
Soil/chemistry
Extreme Environments
Africa, Southern
Biodiversity

@article {pmid39542187,
year = {2025},
author = {Gurumayum, N and Devi, MB and Khound, P and Bhattacharya, A and Sarma, H and Khan, MR and Devi, R},
title = {Bioactive fraction of Musa balbisiana seed mitigates D-galactose-induced brain aging via SIRT1/PGC-1α/FoxO3a activation and intestinal barrier dysfunction by modulating gut microbiota and core metabolites.},
journal = {Free radical biology & medicine},
volume = {226},
number = {},
pages = {43-55},
doi = {10.1016/j.freeradbiomed.2024.11.016},
pmid = {39542187},
issn = {1873-4596},
mesh = {Animals ; *Galactose/adverse effects/toxicity ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Seeds/chemistry ; *Sirtuin 1/metabolism/genetics ; *Plant Extracts/pharmacology ; *Aging/drug effects ; *Oxidative Stress/drug effects ; *Brain/metabolism/drug effects/pathology ; *Forkhead Box Protein O3/metabolism/genetics ; *Musa/chemistry ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Male ; Rats, Sprague-Dawley ; Glycation End Products, Advanced/metabolism ; Antioxidants/pharmacology/metabolism ; },
abstract = {Aging is an inevitable biological process, and emerging research has highlighted the potential of dietary and pharmacological interventions to decelerate the trajectory of age-related diseases and prolong the health span. This study evaluates the protective effects of Musa balbisiana seed on healthy aging using D-galactose-induced accelerated aging rats. The results suggested that the bioactive ethyl acetate fraction of Musa balbisiana seed extract (BF) exhibited protective effects against aging-induced oxidative stress by reducing oxidative DNA damage, advanced glycation end-product formation, and malondialdehyde levels while restoring antioxidant and glyoxalase enzyme activities. BF also ameliorated neurodegeneration by decreasing acetylcholinesterase enzyme activity and amyloid beta plaque formation. Histopathological analysis demonstrated the protective effects of BF against brain aging, liver disruption, renal damage, and intestinal barrier dysfunction. BF further restored intestinal permeability by upregulating the tight junctions (zonula occludens 1 and 2, claudin 1,2,3 and 4, and occludin) and mucin (mucin 2 and mucin 5ac) gene expression while downregulating the expression of inflammatory cytokines (IL-1β, IL-6, and TNF-α). BF significantly induced the phosphorylation of FoxO3a proteins and upregulated the gene expression of SIRT1, PGC-1α, and TFAM in the hippocampus. Next-generation sequencing (NGS) of 16s rRNA amplicons of fecal metagenomics DNA and metabolites profiling showed that BF intervention restructured the gut microbiota and altered core metabolites related to cholesterol metabolism. Overall, our findings demonstrated the multifaceted protective effects of Musa balbisiana seed against D-galactose-induced aging.},
}

Animals
*Galactose/adverse effects/toxicity
*Gastrointestinal Microbiome/drug effects
Rats
*Seeds/chemistry
*Sirtuin 1/metabolism/genetics
*Plant Extracts/pharmacology
*Aging/drug effects
*Oxidative Stress/drug effects
*Brain/metabolism/drug effects/pathology
*Forkhead Box Protein O3/metabolism/genetics
*Musa/chemistry
*Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics
Male
Rats, Sprague-Dawley
Glycation End Products, Advanced/metabolism
Antioxidants/pharmacology/metabolism

@article {pmid39515198,
year = {2024},
author = {De Jaeghere, EA and Hamerlinck, H and Tuyaerts, S and Lippens, L and Van Nuffel, AMT and Baiden-Amissah, R and Vuylsteke, P and Henry, S and Trinh, XB and van Dam, PA and Aspeslagh, S and De Caluwé, A and Naert, E and Lambrechts, D and Hendrix, A and De Wever, O and Van de Vijver, KK and Amant, F and Vandecasteele, K and Verhasselt, B and Denys, HG},
title = {Associations of the gut microbiome with outcomes in cervical and endometrial cancer patients treated with pembrolizumab: Insights from the phase II PRIMMO trial.},
journal = {Gynecologic oncology},
volume = {191},
number = {},
pages = {275-286},
doi = {10.1016/j.ygyno.2024.10.020},
pmid = {39515198},
issn = {1095-6859},
mesh = {Humans ; Female ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Uterine Cervical Neoplasms/drug therapy/microbiology/pathology ; *Endometrial Neoplasms/drug therapy/microbiology/pathology ; *Antineoplastic Agents, Immunological/adverse effects/therapeutic use ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The phase II PRIMMO trial investigated a pembrolizumab-based regimen in patients with recurrent and/or metastatic cervical (CC) or endometrial (EC) carcinoma who had at least one prior line of systemic therapy. Here, exploratory studies of the gut microbiome (GM) are presented.

METHODS: The microbial composition of 77 longitudinal fecal samples obtained from 35 patients (CC, n = 15; EC, n = 20) was characterized using 16S rRNA gene sequencing. Analyses included assessment of alpha (Shannon index) and beta diversity (weighted UniFrac), unbiased hierarchical clustering, and linear discriminant analysis effect size. Correlative studies with demographics, disease characteristics, safety, efficacy, and immune monitoring data were performed.

RESULTS: Significant enrichment in multiple bacterial taxa was associated with the occurrence or resistance to severe treatment-related adverse events (overall or gastrointestinal toxicity specifically). Consistent differences in GM taxonomic composition before pembrolizumab initiation were observed between patients with favorable efficacy (e.g., enriched with Blautia genus) and those with poor efficacy (e.g., enriched with Enterobacteriaceae family and its higher-level taxa up to the phylum level, as well as Clostridium genus and its Clostridiaceae family). Two naturally occurring GM clusters with distinct bacterial compositions were identified. These clusters showed a more than four-fold differential risk for death (hazard ratio, 4.4 [95 % confidence interval, 1.9 to 10.3], P < 0.001) and were associated with interesting (but non-significant) trends in peripheral immune monitoring data.

CONCLUSION: Although exploratory, this study offers initial insights into the intricate interplay between the GM and clinical outcomes in patients with CC and EC treated with a pembrolizumab-based regimen.

TRIAL REGISTRATION: ClinicalTrials.gov (identifier NCT03192059) and EudraCT Registry (number 2016-001569-97).},
}

Humans
Female
*Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Uterine Cervical Neoplasms/drug therapy/microbiology/pathology
*Endometrial Neoplasms/drug therapy/microbiology/pathology
*Antineoplastic Agents, Immunological/adverse effects/therapeutic use
Aged
Adult
Feces/microbiology

@article {pmid39477048,
year = {2024},
author = {Vinayagam, S and Sekar, K and Rajendran, D and Meenakshisundaram, K and Panigrahi, A and Arumugam, DK and Bhowmick, IP and Sattu, K},
title = {The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India.},
journal = {Acta tropica},
volume = {260},
number = {},
pages = {107439},
doi = {10.1016/j.actatropica.2024.107439},
pmid = {39477048},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/microbiology/genetics ; India ; *Phylogeny ; *Gastrointestinal Microbiome ; Mosquito Vectors/microbiology/genetics ; Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Female ; DNA, Ribosomal Spacer/genetics ; },
abstract = {In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.},
}

Animals
*Anopheles/microbiology/genetics
India
*Phylogeny
*Gastrointestinal Microbiome
Mosquito Vectors/microbiology/genetics
Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
Female
DNA, Ribosomal Spacer/genetics

@article {pmid39660058,
year = {2024},
author = {Boer, MD and Melkonian, C and Zafeiropoulos, H and Haas, AF and Garza, DR and Dutilh, BE},
title = {Improving genome-scale metabolic models of incomplete genomes with deep learning.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111349},
pmid = {39660058},
issn = {2589-0042},
abstract = {Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2-9 times for curated models than unweighted gap-filling.},
}

@article {pmid39591453,
year = {2024},
author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L},
title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002921},
pmid = {39591453},
issn = {1545-7885},
mesh = {*Indoleacetic Acids/metabolism ; *Oryza/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Bacteria/metabolism/genetics ; Plant Growth Regulators/metabolism ; Rhizosphere ; Soil Microbiology ; Phylogeny ; Operon/genetics ; Microbiota/physiology ; Seedlings/microbiology/metabolism ; },
abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.},
}

*Indoleacetic Acids/metabolism
*Oryza/microbiology/metabolism
*Arabidopsis/microbiology/metabolism
*Plant Roots/microbiology/metabolism
*Bacteria/metabolism/genetics
Plant Growth Regulators/metabolism
Rhizosphere
Soil Microbiology
Phylogeny
Operon/genetics
Microbiota/physiology
Seedlings/microbiology/metabolism

@article {pmid39513726,
year = {2024},
author = {Zou, L and Zhang, Z and Chen, J and Guo, R and Tong, X and Ju, Y and Lu, H and Yang, H and Wang, J and Zong, Y and Xu, X and Jin, X and Xiao, L and Jia, H and Zhang, T and Liu, X},
title = {Unraveling the impact of host genetics and factors on the urinary microbiome in a young population.},
journal = {mBio},
volume = {15},
number = {12},
pages = {e0277324},
doi = {10.1128/mbio.02773-24},
pmid = {39513726},
issn = {2150-7511},
mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; Metagenomics ; China ; Host Microbial Interactions/genetics ; Urinary Tract/microbiology ; Whole Genome Sequencing ; Urine/microbiology ; Cohort Studies ; Adolescent ; },
abstract = {UNLABELLED: The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1,579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp. PDC80, and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (area under the curve [AUC] = 0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to eight host loci (P < 5 × 10[-8]). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

IMPORTANCE: The urinary microbiome, essential to human health, reveals its unique qualities in our study of 1,579 Chinese individuals. We identified distinctive microbial profiles, or "urotypes," and uncovered strong gender-related influences, particularly from sex hormones, on these microbial communities. Our research highlights significant genetic associations affecting specific urinary bacteria, indicating a deep interaction between our genetics and our microbiome. These insights not only enhance our understanding of the urinary microbiome's role in health and disease but also open new pathways for personalized medical strategies, making our findings crucial for future diagnostic and therapeutic innovations. This work underscores the intricate relationship between our body's biological processes and the microorganisms within, providing valuable knowledge for both scientific and medical communities.},
}

Humans
Female
*Microbiota/genetics
Male
Adult
*Bacteria/genetics/classification/isolation & purification
Young Adult
Metagenomics
China
Host Microbial Interactions/genetics
Urinary Tract/microbiology
Whole Genome Sequencing
Urine/microbiology
Cohort Studies
Adolescent

@article {pmid39319624,
year = {2025},
author = {Shi, Q and Fu, Q and Zhang, J and Hao, G and Liang, C and Duan, F and Ma, J and Zhao, H and Song, W},
title = {Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.},
journal = {Pest management science},
volume = {81},
number = {1},
pages = {266-276},
doi = {10.1002/ps.8429},
pmid = {39319624},
issn = {1526-4998},
support = {2023YFD1400400//National Key R&D Program of China/ ; 2022CXGC020710-6//Subproject of Shandong Province Key R&D Plan Project/ ; QNYCX23027//Qingdao Agricultural University Graduate Student Innovation Program/ ; QNYCX24076//Qingdao Agricultural University Graduate Student Innovation Program/ ; },
mesh = {*Tylenchoidea/physiology ; Animals ; *Paenibacillus polymyxa/genetics/physiology ; *Pseudomonas/physiology ; *Rhizosphere ; *Cucumis sativus/microbiology/parasitology ; *Plant Diseases/prevention & control/parasitology/microbiology ; Soil Microbiology ; Pest Control, Biological ; Microbiota ; },
abstract = {BACKGROUND: Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.

RESULTS: The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.

CONCLUSION: Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.},
}

*Tylenchoidea/physiology
Animals
*Paenibacillus polymyxa/genetics/physiology
*Pseudomonas/physiology
*Rhizosphere
*Cucumis sativus/microbiology/parasitology
*Plant Diseases/prevention & control/parasitology/microbiology
Soil Microbiology
Pest Control, Biological
Microbiota