@article {pmid39629792,
year = {2024},
author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J},
title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.},
journal = {Journal of medical microbiology},
volume = {73},
number = {12},
pages = {},
doi = {10.1099/jmm.0.001940},
pmid = {39629792},
issn = {1473-5644},
mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation & purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.},
}

Humans
*Pharynx/microbiology
*Staphylococcus aureus/isolation & purification/genetics
*Carrier State/microbiology
*Nasal Cavity/microbiology
*Microbiota
*Staphylococcal Infections/microbiology
Male
Female
Adult
Young Adult
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics

@article {pmid39629129,
year = {2024},
author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F},
title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.},
journal = {Theranostics},
volume = {14},
number = {18},
pages = {7219-7240},
pmid = {39629129},
issn = {1838-7640},
mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; },
abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.},
}

Animals
*Sunitinib/toxicity
*Gastrointestinal Microbiome/drug effects
Mice
*Chemical and Drug Induced Liver Injury/pathology/etiology
*Liver/drug effects/pathology
*Mice, Knockout
*Receptors, Cytoplasmic and Nuclear/metabolism
Male
Hepatocytes/drug effects
Mice, Inbred C57BL
Endothelial Cells/drug effects
Apoptosis/drug effects
Bacteroidetes/drug effects
Autophagy/drug effects

@article {pmid39628196,
year = {2024},
author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG},
title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {12},
pages = {7326-7336},
doi = {10.13227/j.hjkx.202312247},
pmid = {39628196},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; },
abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.},
}

*Soil Microbiology
*Fungi/classification
*Bacteria/classification/genetics/growth & development/isolation & purification
Mining
Nitrogen
Soil/chemistry
Phosphorus
Environmental Restoration and Remediation/methods
Microbiota
Ecosystem

@article {pmid39625614,
year = {2024},
author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P},
title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {19},
pmid = {39625614},
issn = {1436-2236},
support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; },
mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation & purification ; },
abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).},
}

*Diethylhexyl Phthalate/metabolism
*Geologic Sediments/microbiology
*Biodegradation, Environmental
*Microbiota
Water Pollutants, Chemical/metabolism
Plastics/metabolism
Gordonia Bacterium/metabolism/genetics
Plasticizers/metabolism
Wetlands
Bacteria/metabolism/classification/genetics/isolation & purification

@article {pmid39623529,
year = {2024},
author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J},
title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.},
journal = {Human vaccines & immunotherapeutics},
volume = {20},
number = {1},
pages = {2430087},
doi = {10.1080/21645515.2024.2430087},
pmid = {39623529},
issn = {2164-554X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy/adverse effects/methods ; Male ; Female ; Middle Aged ; *Rectal Neoplasms/therapy/microbiology ; Aged ; *Feces/microbiology ; Metabolomics ; Metabolome ; Immunotherapy/methods/adverse effects ; Adult ; Chemoradiotherapy/adverse effects/methods ; Metagenomics/methods ; },
abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.},
}

Humans
*Gastrointestinal Microbiome
*Neoadjuvant Therapy/adverse effects/methods
Male
Female
Middle Aged
*Rectal Neoplasms/therapy/microbiology
Aged
*Feces/microbiology
Metabolomics
Metabolome
Immunotherapy/methods/adverse effects
Adult
Chemoradiotherapy/adverse effects/methods
Metagenomics/methods

@article {pmid39550949,
year = {2024},
author = {Wu, ZL and Shi, WJ and Zhang, L and Xia, ZY and Gou, M and Sun, ZY and Tang, YQ},
title = {Investigating the robustness of microbial communities in municipal sludge anaerobic digestion under organic loading rate disturbance.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123326},
doi = {10.1016/j.jenvman.2024.123326},
pmid = {39550949},
issn = {1095-8630},
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Bioreactors/microbiology ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics/classification ; Microbiota ; },
abstract = {Anaerobic digestion (AD) frequently encounters disturbances due to variations in organic loading rates (OLRs), which can result in the failure of the sludge treatment process. However, there is a lack of comprehensive studies on the robustness of AD systems against OLR disturbances and the underlying mechanisms. In this study, the responses of reactor performance and active microbial communities in mesophilic AD were investigated and compared under conditions of OLR shock and OLR fluctuation. Statistical analysis confirmed that all reactors recovered from both types of OLR disturbance, indicating both functional and structural robustness of the mesophilic community. Based on metagenomics and metatranscriptomics analyses, it was observed that high diversity within the microbial community led to functional redundancy, which appears to be a key mechanism contributing to the robustness against OLR disturbances. Additionally, for the first time, the potential metabolic diversity of aerobic autotrophy bacteria in AD reactors was identified, including their roles in the utilization of glucose and acetate. Furthermore, the analysis of topological properties within the microbial interaction network was conducted, and the robustness of the community network was verified through the application of random node deletion attacks. The findings from this study provide valuable information for the effective regulation of microbial communities and the design of practical AD systems.},
}

*Sewage/microbiology
Anaerobiosis
*Bioreactors/microbiology
Waste Disposal, Fluid/methods
Bacteria/metabolism/genetics/classification
Microbiota

@article {pmid39522897,
year = {2024},
author = {Zhang, H and Yang, X and Chen, J and Jiang, Q and Yao, S and Chen, L and Xiang, X},
title = {Investigation of the mechanism by which Tegillarca granosa polysaccharide regulates non-alcoholic fatty liver disease in mice by modulating Lactobacillus Johnsonii.},
journal = {International journal of biological macromolecules},
volume = {282},
number = {Pt 6},
pages = {137259},
doi = {10.1016/j.ijbiomac.2024.137259},
pmid = {39522897},
issn = {1879-0003},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Lactobacillus johnsonii/metabolism ; *Lipid Metabolism/drug effects ; Male ; Disease Models, Animal ; Liver/drug effects/metabolism ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent chronic liver disease, is marked by excessive lipid deposition in the liver without alcohol abuse. Scapharca subcrenatum, a major Chinese farmed bivalve, yields S. subcrenatum polysaccharide (TGP), an active substance with known biological activity. Previous studies revealed TGP's significant regulatory effect on a high-fat diet (HFD)-induced NAFLD in mice. However, the precise mechanisms, particularly involving gut microbiota, remain unclear. In the current study, an antibiotic-treated mouse model was established to determine the mechanistic role of the gut microbiota in the observed anti-obesity effects of TGP. In addition, 16S rRNA genomic and metagenome-derived taxonomic analyses were performed to assess the gut microbial populations. The results showed that TGP selectively enhanced the number of the eosinophilic bacterium Lactobacillus johnsonii, which was reduced in HFD mice. Of note, the oral administration of L. johnsonii formulations to HFD mice alleviated NAFLD, and this was related to regulating lipid metabolism and the accumulation of lipids in the liver. Therefore, the current study uncovered a potential pathway for developing NAFLD treatment strategies based on the interaction between TGP and the gut microbiota.},
}

Animals
*Non-alcoholic Fatty Liver Disease/metabolism/drug therapy
*Polysaccharides/pharmacology/chemistry
Mice
*Gastrointestinal Microbiome/drug effects
*Diet, High-Fat/adverse effects
*Lactobacillus johnsonii/metabolism
*Lipid Metabolism/drug effects
Male
Disease Models, Animal
Liver/drug effects/metabolism
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL

@article {pmid39490096,
year = {2025},
author = {Ji, J and Zhao, Y and Wu, G and Hu, F and Yang, H and Bai, Z and Jin, B and Yang, X},
title = {Responses of endogenous partial denitrification process to acetate and propionate as carbon sources: Nitrite accumulation performance, microbial community dynamic changes, and metagenomic insights.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122680},
doi = {10.1016/j.watres.2024.122680},
pmid = {39490096},
issn = {1879-2448},
mesh = {*Denitrification ; *Nitrites/metabolism ; *Propionates/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; Bioreactors ; Microbiota ; Nitrates/metabolism ; },
abstract = {Endogenous partial denitrification (EPD) offered a promising pathway for supplying nitrite to anammox, and it also enabled energy-efficient and cost-effective nitrogen removal. However, information about the impact of different carbon sources on the EPD system was limited, and the metabolic mechanisms remained unclear. This study operated the EPD system for 180 days with various acetate and propionate ratios over eight phases. The nitrate-to-nitrite transformation ratio (NTR) decreased from 81.7 % to 0.4 % as the acetate/propionate (Ac/Pr) ratio shifted from 3:0 to 0:3, but the NTR returned to 86.1 % after propionate was replaced with acetate. Typical cycles indicated that PHB (126.8 and 133.9 mg COD/g VSS, respectively) was mainly stored, facilitating a higher NTR (87.8 % and 67.7 %, respectively) on days 58 and 180 in the presence of acetate. In contrast, on day 158 in the presence of propionate, PHV (84.8 mg COD/g VSS) was predominantly stored, resulting in negligible nitrite accumulation (0.2 mg N/L). Metagenomic analysis revealed that the microbial community structure did not significantly change, and the (narGHI+napAB)/nirKS ratio consistently exceeded 7:2, despite variations in the carbon source. Compared with acetate, propionate as carbon source reduced the abundance of genes encoding NADH-producing enzymes (e.g., mdh), likely owing to a shift in PHAs synthesis and degradation pathways. Consequently, limited NADH affected electron distribution and transfer rates, thereby decreasing the nitrate reduction rate and causing nitrite produced by narGHI and napAB to be immediately reduced by nirKS. This study provided new insights and guidance for EPD systems to manage the conditions of carbon deficiency or complex carbon sources.},
}

*Denitrification
*Nitrites/metabolism
*Propionates/metabolism
*Carbon/metabolism
*Acetates/metabolism
Bioreactors
Microbiota
Nitrates/metabolism

@article {pmid39427349,
year = {2025},
author = {Zhou, L and Zhang, X and Zhang, X and Wu, P and Wang, A},
title = {Insights into the carbon and nitrogen metabolism pathways in mixed-autotrophy/heterotrophy anammox consortia in response to temperature reduction.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122642},
doi = {10.1016/j.watres.2024.122642},
pmid = {39427349},
issn = {1879-2448},
mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Temperature ; *Autotrophic Processes ; Denitrification ; Heterotrophic Processes ; Microbial Consortia ; Oxidation-Reduction ; },
abstract = {While the multi-coupled anammox system boasts a substantial research foundation, the specific characteristics of its synergistic metabolic response to decreased temperatures, particularly within the range of 13-15 °C, remained elusive. In this study, we delve into the intricate carbon and nitrogen metabolism pathways of mixed-autotrophy/heterotrophy anammox consortia under conditions of temperature reduction. Our macrogenomic analyses reveal a compelling phenomenon: the stimulation of functional genes responsible for complete denitrification, suggesting an enhancement of this process during temperature reduction. This adaptation likely contributes to maintaining system performance amidst environmental challenges. Further metabolic functional recombination analyses highlight a dramatic shift in microbial community composition, with denitrifying MAGs (metagenome-assembled genomes) experiencing a substantial increase in abundance (up to 200 times) compared to autotrophic MAGs. This proliferation underscores the strong stimulatory effect of temperature reduction on denitrifying species. Notably, autotrophic MAGs play a pivotal role in supporting the glycolytic processes of denitrifying MAGs, underscoring the intricate interdependencies within the consortia. Moreover, metabolic variations in amino acid composition among core MAGs emerge as a crucial adaptation mechanism. These differences facilitate the preservation of enzyme activity and enhance the consortia's resilience to low temperatures. Together, these findings offer a comprehensive understanding of the microbial synergistic metabolism within mixed-autotrophy/heterotrophy anammox consortia under temperature reduction, shedding light on their metabolic flexibility and resilience in dynamic environments.},
}

*Nitrogen/metabolism
*Carbon/metabolism
*Temperature
*Autotrophic Processes
Denitrification
Heterotrophic Processes
Microbial Consortia
Oxidation-Reduction

@article {pmid39383807,
year = {2025},
author = {Zhang, Q and Ji, XM and Wang, X and Wang, W and Xu, X and Zhang, Q and Xing, D and Ren, N and Lee, DJ and Chen, C},
title = {Differentiation of the Anammox core microbiome: Unraveling the evolutionary impetus of scalable gene flow.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122580},
doi = {10.1016/j.watres.2024.122580},
pmid = {39383807},
issn = {1879-2448},
mesh = {*Microbiota ; *Gene Flow ; Phylogeny ; Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; Anaerobiosis ; },
abstract = {Anaerobic ammonium oxidation bacteria (AAOB), distinguished by their unique autotrophic nitrogen metabolism, hold pivotal positions in the global nitrogen cycle and environmental biotechnologies. However, the ecophysiology and evolution of AAOB remain poorly understood, attributed to the absence of monocultures. Hence, a comprehensive elucidation of the AAOB-dominated core microbiome, anammox core, is imperative to further completing the theory of engineered nitrogen removal and ecological roles of anammox. Performing taxonomic and phylogenetic analyses on collected genome repertoires, we show here that Candidatus Brocadia and Candidatus Kuenenia possesses a more compact core than Candidatus Jettenia, which partly explains why the latter has a less common ecological presence. Evidence of gene flow is particularly striking in functions related to biosynthesis and oxygen detoxification, underscoring the evolutionary forces driving lineage and core differentiation. Furthermore, CRISPR spacer traceback of the AAOB metagenome-assembled genomes (MAGs) reveals a series of genetic traces for the concealed phages. By reconceptualizing the functional divergence of AAOB with the historical role of phages, we ultimately propose a coevolutionary framework to understand the evolutionary trajectory of anammox microecology. The discoveries provided in this study offer new insights into understanding the evolution of AAOB and the ecology of anammox.},
}

*Microbiota
*Gene Flow
Phylogeny
Ammonium Compounds/metabolism
Oxidation-Reduction
Bacteria/metabolism/genetics
Anaerobiosis

@article {pmid39269772,
year = {2024},
author = {Rahal, Z and Liu, Y and Peng, F and Yang, S and Jamal, MA and Sharma, M and Moreno, H and Damania, AV and Wong, MC and Ross, MC and Sinjab, A and Zhou, T and Chen, M and Tarifa Reischle, I and Feng, J and Chukwuocha, C and Tang, E and Abaya, C and Lim, JK and Leung, CH and Lin, HY and Deboever, N and Lee, JJ and Sepesi, B and Gibbons, DL and Wargo, JA and Fujimoto, J and Wang, L and Petrosino, JF and Ajami, NJ and Jenq, RR and Moghaddam, SJ and Cascone, T and Hoffman, K and Kadara, H},
title = {Inflammation Mediated by Gut Microbiome Alterations Promotes Lung Cancer Development and an Immunosuppressed Tumor Microenvironment.},
journal = {Cancer immunology research},
volume = {12},
number = {12},
pages = {1736-1752},
doi = {10.1158/2326-6066.CIR-24-0469},
pmid = {39269772},
issn = {2326-6074},
support = {R01 CA205608/CA/NCI NIH HHS/United States ; R01 CA248731/CA/NCI NIH HHS/United States ; R01CA248731//National Cancer Institute (NCI)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Lung Neoplasms/immunology/microbiology/pathology ; Mice ; Humans ; *Inflammation/immunology ; Adenocarcinoma of Lung/immunology/microbiology/pathology ; Lipocalin-2/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Mice, Knockout ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences cancer progression and therapy. We recently showed that progressive changes in gut microbial diversity and composition are closely coupled with tobacco-associated lung adenocarcinoma in a human-relevant mouse model. Furthermore, we demonstrated that the loss of the antimicrobial protein Lcn2 in these mice exacerbates protumor inflammatory phenotypes while further reducing microbial diversity. Yet, how gut microbiome alterations impinge on lung adenocarcinoma development remains poorly understood. In this study, we investigated the role of gut microbiome changes in lung adenocarcinoma development using fecal microbiota transfer and delineated a pathway by which gut microbiome alterations incurred by loss of Lcn2 fostered the proliferation of proinflammatory bacteria of the genus Alistipes, triggering gut inflammation. This inflammation propagated systemically, exerting immunosuppression within the tumor microenvironment, augmenting tumor growth through an IL6-dependent mechanism and dampening response to immunotherapy. Corroborating our preclinical findings, we found that patients with lung adenocarcinoma with a higher relative abundance of Alistipes species in the gut showed diminished response to neoadjuvant immunotherapy. These insights reveal the role of microbiome-induced inflammation in lung adenocarcinoma and present new potential targets for interception and therapy.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Tumor Microenvironment/immunology
*Lung Neoplasms/immunology/microbiology/pathology
Mice
Humans
*Inflammation/immunology
Adenocarcinoma of Lung/immunology/microbiology/pathology
Lipocalin-2/metabolism
Mice, Inbred C57BL
Disease Models, Animal
Fecal Microbiota Transplantation
Mice, Knockout

@article {pmid39146704,
year = {2024},
author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T},
title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {52},
number = {},
pages = {101309},
doi = {10.1016/j.cbd.2024.101309},
pmid = {39146704},
issn = {1878-0407},
mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; },
abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.},
}

Animals
*Bombyx/microbiology/genetics
*Enterococcus/genetics
*Gastrointestinal Microbiome
*Intestines/microbiology
Proteomics
Symbiosis
Multiomics

@article {pmid39002350,
year = {2024},
author = {Lai, KP and Boncan, DAT and Qin, X and Chan, TF and Tse, WKF},
title = {Roles and occurrences of microbiota in the osmoregulatory organs, gills and gut, in marine medaka upon hypotonic stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {52},
number = {},
pages = {101285},
doi = {10.1016/j.cbd.2024.101285},
pmid = {39002350},
issn = {1878-0407},
mesh = {Animals ; *Gills/microbiology/metabolism ; *Osmoregulation ; *Oryzias/microbiology ; Osmotic Pressure ; Seawater/microbiology ; Gastrointestinal Microbiome ; Microbiota ; Fresh Water/microbiology ; },
abstract = {Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na[+]/K[+]-atpase, and cftr, were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress.},
}

Animals
*Gills/microbiology/metabolism
*Osmoregulation
*Oryzias/microbiology
Osmotic Pressure
Seawater/microbiology
Gastrointestinal Microbiome
Microbiota
Fresh Water/microbiology

@article {pmid39621710,
year = {2024},
author = {Mangoma, N and Zhou, N and Ncube, T},
title = {Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0299620},
doi = {10.1371/journal.pone.0299620},
pmid = {39621710},
issn = {1932-6203},
mesh = {Zimbabwe ; *Metagenome ; *Phylogeny ; Metagenomics/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Ecosystem ; Microbiota/genetics ; Extreme Environments ; },
abstract = {The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.},
}

Zimbabwe
*Metagenome
*Phylogeny
Metagenomics/methods
Bacteria/genetics/classification
Genome, Bacterial
Ecosystem
Microbiota/genetics
Extreme Environments

@article {pmid39621607,
year = {2024},
author = {Deel, HL and Manter, DK and Moore, JM},
title = {Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0314072},
doi = {10.1371/journal.pone.0314072},
pmid = {39621607},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Machine Learning ; Ecosystem ; Genes, Microbial ; },
abstract = {Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.},
}

*Soil Microbiology
*Soil/chemistry
*RNA, Ribosomal, 16S/genetics
Metagenome
Bacteria/genetics/classification/isolation & purification
Microbiota/genetics
Machine Learning
Ecosystem
Genes, Microbial

@article {pmid39621089,
year = {2024},
author = {Singh, K and Gupta, JK and Chanchal, DK and Shinde, MG and Kumar, S and Jain, D and Almarhoon, ZM and Alshahrani, AM and Calina, D and Sharifi-Rad, J and Tripathi, A},
title = {Natural products as drug leads: exploring their potential in drug discovery and development.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {39621089},
issn = {1432-1912},
abstract = {Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.},
}

@article {pmid39620486,
year = {2024},
author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X},
title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.},
journal = {Virulence},
volume = {15},
number = {1},
pages = {2428843},
doi = {10.1080/21505594.2024.2428843},
pmid = {39620486},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation & purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; },
abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Metagenomics
*Anti-Bacterial Agents/pharmacology/therapeutic use
Male
Female
Adult
Middle Aged
Feces/microbiology
Bacteria/genetics/drug effects/classification/isolation & purification
Leukemia/drug therapy/microbiology/complications
Drug Resistance, Microbial/genetics
Aged
Young Adult
Antineoplastic Agents/adverse effects

@article {pmid39620359,
year = {2024},
author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P},
title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2429267},
doi = {10.1080/19490976.2024.2429267},
pmid = {39620359},
issn = {1949-0984},
mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; },
abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.},
}

Animals
Female
Pregnancy
*Gastrointestinal Microbiome
Mice
*Feces/microbiology
*Autophagy-Related Proteins/genetics/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Intestinal Mucosa/microbiology/metabolism
Epithelial Cells/microbiology/metabolism
Crohn Disease/microbiology/metabolism
Mice, Inbred C57BL
Metagenomics
Chemokine CXCL1/genetics/metabolism

@article {pmid39619205,
year = {2024},
author = {Hewson, I and Brandt, M and Budd, K and Breitbart, M and DeRito, C and Gittens, S and Henson, MW and Hylkema, A and Sevier, M and Souza, M and Vilanova-Cuevas, B and Von Hoene, S},
title = {Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18321},
pmid = {39619205},
issn = {2167-8359},
mesh = {Animals ; *Metagenomics ; Caribbean Region ; *Genome, Viral/genetics ; Echinodermata/virology ; Metagenome ; Holothuria/virology/genetics ; Coral Reefs ; Viruses/genetics/isolation & purification/classification ; Virome/genetics ; },
abstract = {BACKGROUND: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.

METHODS: We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.

RESULTS: D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.},
}

Animals
*Metagenomics
Caribbean Region
*Genome, Viral/genetics
Echinodermata/virology
Metagenome
Holothuria/virology/genetics
Coral Reefs
Viruses/genetics/isolation & purification/classification
Virome/genetics

@article {pmid39510362,
year = {2024},
author = {Deng, YP and Yao, C and Fu, YT and Zhuo, Y and Zou, JL and Pan, HY and Peng, YY and Liu, GH},
title = {Analyses of the gut microbial composition of domestic pig louse Haematopinus suis.},
journal = {Microbial pathogenesis},
volume = {197},
number = {},
pages = {107106},
doi = {10.1016/j.micpath.2024.107106},
pmid = {39510362},
issn = {1096-1208},
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Swine Diseases/microbiology/parasitology ; Metagenomics ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Haematopinus suis is an obligatory ectoparasite of the domestic pig, serving as a vector of several swine pathogens and posing great threats to the pig industry. The gut microbiome of lice is thought of an important mediator of their healthy physiology. However, there is a great paucity of lice-associated microbial communities' structure and function. The current study aimed to profile the gut microbiome and to understand the microbial functions of swine lice by metagenomic sequencing and bioinformatics analyses. In total, 102,358 (77.2 %) nonredundant genes were cataloged, by contrast, only a small proportion of genes were assigned to microbial taxa and functional assemblages. Bacteria of known or potential public health significance such as Anaplasma phagocytophilum, Chlamydia trachomatis, Waddlia chondrophila, Bacillus cereus, and Leptotrichia goodfellowii were observed in all samples. The integrated microbial profile further illustrated the evolutionary relevance of endosymbionts and detailed the functional composition, and findings suggested H. suis may acquire adenosylcobalamin by feeding due to an adenosylcobalamin synthesis defect and a lack of complete synthases of endosymbionts. Sucking lice contained fewer functional genes compared with ticks and fleas probably because of the obligate host specificity of parasitic lice. In addition, the genes from the intestines contained encompassed most of the microbial functional genes in sucking lice. A wide range of unknown taxonomic and functional assemblages were discovered, which improves our understanding related to microbial features and physiological activities of sucking lice. In general, this study increases the characterization of the microbiota of lice and offers clues for preventing and controlling lice infestation in swine production in the future.},
}

Animals
Swine
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
Symbiosis
Phylogeny
Swine Diseases/microbiology/parasitology
Metagenomics
Computational Biology
RNA, Ribosomal, 16S/genetics

@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {14},
number = {12},
pages = {1972-1984},
doi = {10.1002/2211-5463.13881},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}

Animals
Japan
*Gastrointestinal Microbiome/genetics
*Birds/microbiology/virology
*Metagenomics/methods
Feces/microbiology
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Metagenome/genetics

@article {pmid39616358,
year = {2024},
author = {Dell'Olio, A and Scott, WT and Taroncher-Ferrer, S and San Onofre, N and Soriano, JM and Rubert, J},
title = {Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {250},
pmid = {39616358},
issn = {2049-2618},
support = {79441//'European Union's Horizon 2020 Research and Innovation programme' for the Marie Skłodowska-Curie/ ; RYC2018-024850-I//Spanish Ministry of Science and Innovation for the Ramón y Cajal fellowship/ ; },
mesh = {*Dietary Fiber/metabolism ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; *Malus/microbiology ; Humans ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Pectins/metabolism ; Metabolomics ; Cellulose/metabolism ; Bioreactors/microbiology ; Multiomics ; },
abstract = {BACKGROUND: Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.

RESULTS: Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.

CONCLUSION: We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.},
}

*Dietary Fiber/metabolism
*Obesity/microbiology
*Gastrointestinal Microbiome
*Malus/microbiology
Humans
Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics
Pectins/metabolism
Metabolomics
Cellulose/metabolism
Bioreactors/microbiology
Multiomics

@article {pmid39616151,
year = {2024},
author = {Wang, J and Zhong, H and Chen, Q and Ni, J},
title = {Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {141},
pmid = {39616151},
issn = {2055-5008},
support = {52070002, 51721006, 51925901//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52209078//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023T160020//China Postdoctoral Science Foundation/ ; },
mesh = {*Groundwater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Salinity ; Biodiversity ; Metagenome ; Adaptation, Physiological ; Nitrogen/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Metagenomics/methods ; Bacterial Physiological Phenomena ; },
abstract = {Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.},
}

*Groundwater/microbiology
*Bacteria/genetics/classification/isolation & purification
*Phylogeny
Salinity
Biodiversity
Metagenome
Adaptation, Physiological
Nitrogen/metabolism
Carbon/metabolism
Sulfur/metabolism
Metagenomics/methods
Bacterial Physiological Phenomena

@article {pmid39571342,
year = {2024},
author = {Calvani, R and Giampaoli, O and Marini, F and Del Chierico, F and De Rosa, M and Conta, G and Sciubba, F and Tosato, M and Picca, A and Ciciarello, F and Galluzzo, V and Gervasoni, J and Di Mario, C and Santoro, L and Tolusso, B and Spagnoli, M and Tomassini, A and Aureli, W and Toto, F and Pane, S and Putignani, L and Miccheli, A and Marzetti, E and Landi, F and , },
title = {Beetroot juice intake positively influenced gut microbiota and inflammation but failed to improve functional outcomes in adults with long COVID: A pilot randomized controlled trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {43},
number = {12},
pages = {344-358},
doi = {10.1016/j.clnu.2024.11.023},
pmid = {39571342},
issn = {1532-1983},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Beta vulgaris/chemistry ; *Fruit and Vegetable Juices ; Pilot Projects ; Adult ; Double-Blind Method ; Middle Aged ; *COVID-19 ; *Inflammation ; Dietary Supplements ; Nitrates ; SARS-CoV-2 ; Young Adult ; },
abstract = {BACKGROUND & AIMS: Long-term effects of coronavirus disease 2019 (long COVID) develop in a substantial number of people following an acute COVID-19 episode. Red beetroot juice may have positive effects on multiple pathways involved in long COVID. The aim of this pilot study was to explore the impact of beetroot juice supplementation on physical function, gut microbiota, and systemic inflammation in adults with long COVID.

METHODS: A single-center, double-blind, placebo-controlled randomized trial was conducted to test the effects of 14 days of beetroot juice supplementation, rich in nitrates and betalains, on functional and biological outcomes in adults aged between 20 and 60 years with long COVID. Participants were randomized 1:1 to receive either daily oral supplementation with 200 mL beetroot juice (∼600 mg nitrate) or placebo (∼60 mg nitrate) for 14 days. The primary endpoint was the change from baseline to day 14 in a fatigue resistance test. Secondary outcomes included the distance walked on the 6-min walk test, handgrip strength, and flow-mediated dilation. Secondary endpoints also included changes from baseline in circulating inflammatory mediators and metagenomic and fecal water metabolomic profiles. Partial least squares discriminant analysis (PLS-DA) models were built to evaluate the differences in biological variables associated with the interventions.

RESULTS: Thirty-one participants were randomized in the study. Twenty-five of them (median (interquartile range) age 40 (10), 14 [56 %] women), received either beetroot juice (15) or placebo (10) and completed the study. At 14 days, fatigue resistance significantly improved from baseline (mean difference [standard error]: +21.8 [3.7] s; p < 0.001) with no significant differences between intervention groups. A significant increase from baseline in the distance walked on the 6-min walk test was observed (mean difference [standard error]: +30.0 [9.4] m; p = 0.03), which was not different between groups. Flow-mediated dilation did not differ between participants who received beetroot juice and those on placebo. PLS-DA models allowed correct classification of participants with 92.2 ± 4.4 % accuracy. Those who ingested red beetroot juice had a greater abundance of bacteria with well-known beneficial effects, including Akkermansia, Oscillospira, Prevotella, Roseburia, Ruminococcaceae, and Turicibacter, compared with placebo. Participants allocated to beetroot juice supplementation were also characterized by significantly higher levels of fecal nicotinate, trimethylamine, and markers of beetroot juice intake (e.g., 5,6-dihydroxyindole). Finally, higher levels of interferon gamma and macrophage inflammatory protein-1β were found in participants who consumed beetroot juice.

CONCLUSION: Beetroot juice supplementation for two weeks did not to induce significant improvements in functional outcomes in adults with long COVID compared with placebo. Beneficial effects were observed in both gut microbiota composition (i.e., increase in probiotic species) and inflammatory mediators.

TRIAL REGISTRATION: Trial was registered under ClinicalTrials.gov. Identifier no. NCT06535165.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Beta vulgaris/chemistry
*Fruit and Vegetable Juices
Pilot Projects
Adult
Double-Blind Method
Middle Aged
*COVID-19
*Inflammation
Dietary Supplements
Nitrates
SARS-CoV-2
Young Adult

@article {pmid39481794,
year = {2024},
author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q},
title = {Methodology comparison of environmental sediment fungal community analysis.},
journal = {Environmental research},
volume = {263},
number = {Pt 3},
pages = {120260},
doi = {10.1016/j.envres.2024.120260},
pmid = {39481794},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation & purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; },
abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.},
}

*Geologic Sediments/microbiology
*Fungi/genetics/isolation & purification/classification
*RNA, Ribosomal, 18S/genetics
*High-Throughput Nucleotide Sequencing
DNA, Fungal/analysis
DNA, Ribosomal Spacer/genetics
Mycobiome
Rivers/microbiology

@article {pmid39374753,
year = {2024},
author = {Pushkareva, E and Hejduková, E and Elster, J and Becker, B},
title = {Microbial response to seasonal variation in arctic biocrusts with a focus on fungi and cyanobacteria.},
journal = {Environmental research},
volume = {263},
number = {Pt 2},
pages = {120110},
doi = {10.1016/j.envres.2024.120110},
pmid = {39374753},
issn = {1096-0953},
mesh = {Arctic Regions ; *Seasons ; *Cyanobacteria/genetics ; *Fungi/genetics/classification ; *Microbiota ; Ecosystem ; },
abstract = {Biocrusts are crucial components of Arctic ecosystems, playing significant roles in carbon and nitrogen cycling, especially in regions where plant growth is limited. However, the microbial communities within Arctic biocrusts and their strategies for surviving the harsh conditions remain poorly understood. In this study, the microbial profiles of Arctic biocrusts across different seasons (summer, autumn, and winter) were investigated in order to elucidate their survival strategies in extreme conditions. Metagenomic and metatranscriptomic analyses revealed significant differences in microbial community composition among the sites located in different elevations. The bacterial communities were dominated by Actinobacteria and Proteobacteria, while the fungal communities were mainly represented by Ascomycota and Basidiomycota, with lichenized and saprotrophic traits prevailing. Cyanobacteria were primarily composed of heterocystous cyanobacteria. Furthermore, the study identified molecular mechanisms underlying cold adaptation, including the expression of heat shock proteins and cold-inducible RNA helicases in cyanobacteria and fungi. Overall, the microbial communities appear to be permanently well adapted to the extreme environment.},
}

Arctic Regions
*Seasons
*Cyanobacteria/genetics
*Fungi/genetics/classification
*Microbiota
Ecosystem

@article {pmid39367927,
year = {2024},
author = {Wang, Q and Wang, M and Chen, Y and Miao, Q and Jin, W and Ma, Y and Pan, J and Hu, B},
title = {Deciphering microbiome and fungi-bacteria interactions in chronic wound infections using metagenomic sequencing.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {43},
number = {12},
pages = {2383-2396},
pmid = {39367927},
issn = {1435-4373},
support = {20YF1407700//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; },
mesh = {Humans ; Male ; Female ; *Wound Infection/microbiology ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing ; Chronic Disease ; Adult ; Microbial Interactions ; Mycobiome/genetics ; Aged, 80 and over ; },
abstract = {PURPOSE: Chronic wounds caused by infections impose a considerable global healthcare burden. The microbial features of these infections and possible correlations between bacteria and fungi may influence wound healing. However, metagenomic next-generation sequencing (mNGS) analyses of these features remain sparse. Therefore, we performed mNGS on chronic wound infection samples to investigate features and correlations between the bacteriome and mycobiome in 66 patients (28: chronic wounds; 38: non-chronic wounds).

METHODS: Microbial community characteristics in patients with wound infections, microbiome-systemic inflammation associations, and bacteria-fungi correlations were analyzed.

RESULTS: Infections constituted the primary cause of wounds in this study. Nontuberculous mycobacteria (23%) and Mycobacterium tuberculosis (13%) were the most common pathogens associated with chronic wounds, whereas Staphylococcus aureus (15%) was the most prevalent in non-chronic wound infections. Patients with chronic wound infections had a higher abundance of Pseudomonas aeruginosa than those without chronic wounds. Microbes with a high relative abundance in chronic wound infections were less significantly associated with plasma inflammatory factors than those in non-chronic wound infections. Additionally, a positive correlation between Candida glabrata and P. aeruginosa and an association between Malassezia restricta and anaerobic species were detected in patients with chronic wound infections.

CONCLUSION: Our results further support the hypothesis that P. aeruginosa is a microbial biomarker of chronic wound infection regardless of the causative pathogens. Moreover, we propose a positive correlation between C. glabrata and P. aeruginosa in chronic wound infections, which advances the current understanding of fungi-bacteria correlations in patients with chronic wound infections.},
}

Humans
Male
Female
*Wound Infection/microbiology
Middle Aged
*Fungi/classification/genetics/isolation & purification
Aged
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
*High-Throughput Nucleotide Sequencing
Chronic Disease
Adult
Microbial Interactions
Mycobiome/genetics
Aged, 80 and over

@article {pmid38857786,
year = {2024},
author = {Zhou, Y and Guo, L and Xiao, T and Chen, Y and Lv, T and Wang, Y and Zhang, S and Cai, H and Chi, X and Kong, X and Zhou, K and Shen, P and Xiao, Y},
title = {Characterization and dynamics of intestinal microbiota in patients with Clostridioides difficile colonization and infection.},
journal = {Microbes and infection},
volume = {26},
number = {8},
pages = {105373},
doi = {10.1016/j.micinf.2024.105373},
pmid = {38857786},
issn = {1769-714X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology ; *Clostridioides difficile ; Female ; Male ; Middle Aged ; Dysbiosis/microbiology ; Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Metagenomics ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Bacteroidetes/isolation & purification ; Aged, 80 and over ; },
abstract = {Gut microbiota dysbiosis increases the susceptibility to Clostridioides difficile infection (CDI). In this study, we monitored C. difficile colonization (CDC) patients from no CDC status (CDN) to CDC status (CDCp) and CDI patients from asymptomatic status before CDI (PRECDI), CDI status (ONCDI), to asymptomatic status after CDI (POSTCDI). Based on metagenomic sequencing, we aimed to investigate the interaction pattern between gut microbiota and C. difficile. There was no significant difference of microbiota diversity between CDN and CDCp. In CDCp, Bacteroidetes and short-chain fatty acid (SCFA)-producing bacteria increased, with a positive correlation between SCFA-producing bacteria and C. difficile colonization. Compared with PRECDI, ONCDI and POSTCDI showed a significant decrease in microbiota diversity, particularly in Bacteroidetes and SCFA-producing bacteria, with a positive correlation between opportunistic pathogen and C. difficile. Fatty acid metabolism, and amino acid biosynthesis were enriched in CDN, CDCp, and PRECDI, while bile secretion was enriched in ONCDI and POSTCDI. Microbiota and metabolic pathways interaction networks in CDN and CDCp were more complex, particularly pathways in fatty acid and bile acid metabolism. Increasing of Bacteroidetes and SCFA-producing bacteria, affecting amino acid and fatty acid metabolism, is associated with colonization resistance to C. difficile and inhibiting the development of CDI.},
}

Humans
*Gastrointestinal Microbiome
*Clostridium Infections/microbiology
*Clostridioides difficile
Female
Male
Middle Aged
Dysbiosis/microbiology
Aged
Bacteria/classification/isolation & purification/genetics/metabolism
Adult
Metagenomics
Feces/microbiology
Fatty Acids, Volatile/metabolism
Bacteroidetes/isolation & purification
Aged, 80 and over

@article {pmid39614549,
year = {2024},
author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G},
title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115030},
doi = {10.1016/j.foodres.2024.115030},
pmid = {39614549},
issn = {1873-7145},
mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; },
abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.},
}

*Bacteria/genetics/classification/metabolism
*Food Microbiology
Humans
Soy Foods/microbiology
Fermentation
Rhizopus/genetics/metabolism
Hygiene
Indonesia
Microbiota
Fermented Foods/microbiology

@article {pmid39614478,
year = {2024},
author = {Yu, H and Li, Z and Zheng, D and Chen, C and Ge, C and Tian, H},
title = {Exploring microbial dynamics and metabolic pathways shaping flavor profiles in Huangjiu through metagenomic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115036},
doi = {10.1016/j.foodres.2024.115036},
pmid = {39614478},
issn = {1873-7145},
mesh = {*Taste ; *Metagenomics/methods ; *Fermentation ; *Wine/microbiology/analysis ; *Metabolic Networks and Pathways ; Microbiota/genetics ; Oryza/microbiology ; Flavoring Agents/metabolism ; Humans ; Food Microbiology ; Odorants/analysis ; Male ; },
abstract = {In the production of Huangjiu (Chinese rice wine), fermentation microbiota plays a crucial role in flavor formation. This study investigates the microbial dynamics and metabolic pathways that shape the flavor profiles of Huangjiu using different starters. Sensory evaluation and metabolite analysis of six starters revealed significant differences in ester, fruity, and sweet aromas. Saccharomyces, Aspergillus, and Rhizopus were identified as the dominant genera significantly impacting fermentation. Metagenomic species and functional gene annotations of Huangjiu starters elucidated the metabolic pathways for key flavor compounds synthesis pathways. Enzyme genes involved in these pathways were classified and annotated to microbial genera using the NR database, identifying 231 classes of relevant catalytic enzymes and 154 microbial genera. A metabolic relationship between flavor compound formation and different microbial genera was established using catalytic enzymes as a bridge. This study highlights the impact of starter composition on the final product and provides new insights for optimizing starters to enhance Huangjiu flavor quality.},
}

*Taste
*Metagenomics/methods
*Fermentation
*Wine/microbiology/analysis
*Metabolic Networks and Pathways
Microbiota/genetics
Oryza/microbiology
Flavoring Agents/metabolism
Humans
Food Microbiology
Odorants/analysis
Male

@article {pmid39614477,
year = {2024},
author = {Yang, L and Fan, W and Xu, Y},
title = {Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115034},
doi = {10.1016/j.foodres.2024.115034},
pmid = {39614477},
issn = {1873-7145},
mesh = {*Seasons ; *Hot Temperature ; *Food Storage/methods ; *Microbiota ; Fermentation ; Bacteria/metabolism/classification ; Food Microbiology ; Metabolomics ; Proteomics ; China ; Metagenomics ; Camellia sinensis/microbiology/metabolism ; Fungi/metabolism/classification ; },
abstract = {Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.},
}

*Seasons
*Hot Temperature
*Food Storage/methods
*Microbiota
Fermentation
Bacteria/metabolism/classification
Food Microbiology
Metabolomics
Proteomics
China
Metagenomics
Camellia sinensis/microbiology/metabolism
Fungi/metabolism/classification

@article {pmid39614169,
year = {2024},
author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z},
title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {505},
pmid = {39614169},
issn = {1471-2180},
mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; },
abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.

METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.

RESULTS: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80).

CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.},
}

Humans
*Dust/analysis
Male
Child
Female
*Rhinitis, Allergic/microbiology
Case-Control Studies
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/isolation & purification/genetics
*Skin/microbiology
*Mouth/microbiology
*Microbiota
Nasal Cavity/microbiology
Air Pollution, Indoor/analysis
Child, Preschool
Metagenomics/methods
Nose/microbiology

@article {pmid39614167,
year = {2024},
author = {Mangoma, N and Zhou, N and Ncube, T},
title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {510},
pmid = {39614167},
issn = {1471-2180},
mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation & purification ; Water Microbiology ; },
abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.

RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.

CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.},
}

Zimbabwe
*Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Salinity
Phylogeny
Hydrogen-Ion Concentration
Archaea/genetics/classification/metabolism/isolation & purification
Water Microbiology

@article {pmid39536943,
year = {2024},
author = {Fadell, F and Saliba, R and El-Solh, AA},
title = {Bacteriology of Aspiration Pneumonia: The Lung Microbiome and the Changing Microbial Etiology.},
journal = {Seminars in respiratory and critical care medicine},
volume = {45},
number = {6},
pages = {626-633},
doi = {10.1055/s-0044-1792111},
pmid = {39536943},
issn = {1098-9048},
mesh = {Humans ; *Pneumonia, Aspiration/microbiology ; *Microbiota ; Lung/microbiology ; Dysbiosis/microbiology ; },
abstract = {Aspiration pneumonia refers to the process of alveolar inflammation induced by the inhalation of oropharyngeal secretions into the lower respiratory tract. Predisposing factors comprise swallowing dysfunction, impaired cough reflex, and degenerative neurological diseases. Accumulating evidence projects a fading contribution of anaerobic bacteria in aspiration pneumonia at the expense of Gram-negative bacilli, with Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, becoming the predominant organisms recovered from respiratory specimens. Aspiration of oropharyngeal secretions colonized with respiratory pathogens induces a profound disequilibrium of the lung microbiota resulting in a state of dysbiosis. Understanding this complex temporal variability between microbiome-host associations was only made possible with the introduction of metagenomic sequencing. In this narrative review, we summarize existing knowledge and elaborate on the evolving microbiology of aspiration pneumonia including the link between oral microbiome and pulmonary aspiration. We also highlight the progress and challenges in instituting microbiome-targeted strategies for preventing and treating the sequelae of aspiration pneumonia.},
}

Humans
*Pneumonia, Aspiration/microbiology
*Microbiota
Lung/microbiology
Dysbiosis/microbiology

@article {pmid39486340,
year = {2024},
author = {Zhang, H and Cheng, S and Yan, W and Zhang, Q and Jiang, B and Xing, Y and Zhang, B},
title = {Interplay between vanadium distribution and microbial community in soil-plant system.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136303},
doi = {10.1016/j.jhazmat.2024.136303},
pmid = {39486340},
issn = {1873-3336},
mesh = {*Vanadium/metabolism ; *Soil Microbiology ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Microbiota ; Bacteria/metabolism/genetics/classification ; Biodegradation, Environmental ; Plant Roots/microbiology/metabolism ; },
abstract = {Soil-plant system play an essential role in distribution and transformation of vanadium (V). V shapes the diversity of soil communities, while soil microorganisms mediate V transformation. Plants also absorb V from surrounding soil. However, the study of microbial response to V stress in different soil-plant compartments is limited, and the metabolic functions driving V transformation across these systems remain elusive. The study investigates the distribution of V in soil-plant systems nearby a V smelter. 16S rRNA sequencing and metagenomics are utilized to reveal the microbial adaptation and V transformation in bulk soil, rhizosphere, and endosphere. Bothriochloa ischaemum (L.) Keng. (BK) exhibits higher phytoextraction potential (TF = 0.74 ± 0.26). Environmental variables, including pH, V, OM, and AP, show significant (p < 0.05) influence in soil community composition, with homogeneous selection governing the assembly processes in bulk soil and rhizosphere, while stochastic process dominates endospheric assembly. Metagenomic investigation revealed a coordinated metabolic pathway between functional taxa in soil and plants, which lead to root uptake and translocation. V stress is mitigated through Nocardioide, Microvirga, and Solirubrobacter, putatively harboring V(V) reduction genes n arG and mtrC in soil. In rhizosphere, citrate synthase gltA and alkaline phosphatase phoD exhibit functional potential to facilitate formation of V-complexation to increase V mobility. In endoshere, endophytic Enterobacter further detoxifies V(V), and likely promotes V translocation through siderophore biosynthesis gene, iucA. These findings enhance our understanding on interplay between V and microbial community in soil-plant systems, which is instrumental in developing mitigation plan for V contaminated sites.},
}

*Vanadium/metabolism
*Soil Microbiology
*Soil Pollutants/metabolism
RNA, Ribosomal, 16S/genetics
Rhizosphere
Microbiota
Bacteria/metabolism/genetics/classification
Biodegradation, Environmental
Plant Roots/microbiology/metabolism

@article {pmid39405686,
year = {2024},
author = {Zhang, S and Hou, R and Wang, Y and Huang, Q and Lin, L and Li, H and Liu, S and Jiang, Z and Huang, X and Xu, X},
title = {Xenobiotic metabolism activity of gut microbiota from six marine species: Combined taxonomic, metagenomic, and in vitro transformation analysis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136152},
doi = {10.1016/j.jhazmat.2024.136152},
pmid = {39405686},
issn = {1873-3336},
mesh = {Animals ; *Xenobiotics/metabolism/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/genetics/metabolism/classification ; Water Pollutants, Chemical/metabolism/toxicity ; RNA, Ribosomal, 16S/genetics ; Fishes/microbiology/metabolism ; Metagenomics ; Bivalvia/microbiology/metabolism ; Biotransformation ; },
abstract = {The xenobiotic metabolism driven by the gut microbiota significantly regulates the bioavailability and toxic effects of environmental pollutants such as plasticizers on aquatic organisms. However, it is still unknown whether the gut microbiota can exhibit variable metabolic ability across host species and which functional bacteria and genes are involved in xenobiotic transformation. This study investigated the enriched gut microbiota community composition and diversity of in vitro enrichment cultures from 6 marine species, namely, yellowfin seabream (Acanthopagrus latus), thorn fish (Terapon jarbua), shortnose ponyfish (Leiognathus brevirostris), mussel (Perna viridis), prawn (Parapenaeopsis hungerfordi) and crab (Charybdis riversandersoni). Pseudomonadota, Bacteroidota and Bacillota were the dominant phyla and Enterobacter, Raoultella, Klebsiella, Dysgonomanas and Lactococcus were the dominant genera in the enriched flora according to 16S rRNA sequencing. Furthermore, the metagenomic results revealed that all enriched gut microbiota presented metabolic genes for carbohydrates, amino acids, lipids, and xenobiotics. In particular, the gut microbiota of yellowfin seabream had the highest abundance of glycoside hydrolase family genes and CYP450 enzyme genes. Klebsiella was identified as a common potential degrader of xenobiotic metabolism. In addition, the Biolog plate test system confirmed that the gut microbiota can metabolize various carbon sources and drive the xenobiotic transformation. According to AWCD analysis of community level physiological profiling (CLPP), yellowfin seabream > mussel > prawn > shortnose ponyfish > crab > thorn fish. The gut microbiota of yellowfin seabream presented a stronger metabolic profile of phthalates and bisphenol analogs which reflected by their AWCD results and concentration variations. Overall, our results demonstrated the diverse metabolic abilities of the gut microbiota from six marine organisms and their potential for altering of the fate of xenobiotics in the ecosystem on the basis of combined taxonomic, metagenomic, and in vitro transformation analysis.},
}

Animals
*Xenobiotics/metabolism/toxicity
*Gastrointestinal Microbiome/drug effects
*Bacteria/genetics/metabolism/classification
Water Pollutants, Chemical/metabolism/toxicity
RNA, Ribosomal, 16S/genetics
Fishes/microbiology/metabolism
Metagenomics
Bivalvia/microbiology/metabolism
Biotransformation

@article {pmid39405675,
year = {2024},
author = {Xing, BS and Su, YM and Fu, YL and Wu, YF and Yan, CH and Wang, XC and Li, YY and Chen, R},
title = {Comparison of the short- and long-term effects of zinc ions on the anaerobic mesophilic co-digestion of food waste and waste activated sludge: Digester performance, antibiotic resistance gene reduction and the microbial community.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136119},
doi = {10.1016/j.jhazmat.2024.136119},
pmid = {39405675},
issn = {1873-3336},
mesh = {*Zinc ; *Sewage/microbiology ; Anaerobiosis ; *Bioreactors ; *Methane/metabolism ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Food ; Waste Disposal, Fluid/methods ; Food Loss and Waste ; },
abstract = {Heavy metals contained in waste activated sludge (WAS), especially zinc ions, have an inhibitory effect on the anaerobic digestion. However, the effects of zinc ions on digester performance, antibiotic resistance genes (ARGs) reduction, and the microbial community involved in the anaerobic mesophilic co-digestion (AcoD) of WAS and food waste (FW) have not been fully characterized. Therefore, batch trials and continuous stirred tank reactors were used under different zinc-ion concentrations. Findings showed that the AcoD system can tolerate a maximum zinc ion of 540 mg/L in a short-term batch and 470 mg/L in a long-term AcoD system, promoting methane production of approximately 1.0-17.0 %. Metagenomic analysis revealed that syntrophic H2 transfer occurred between Syntrophomonas and Methanoculleus and the aceticlastic and hydrogenotrophic methanogenic pathways were both enhanced by 1.18- and 1.16 times, respectively. Moreover, the relative abundance of Methanosarcina increased from 58.4 % to 72.5 % at 470 mg/L to adapt to the high zinc ion concentration during long-term continuous operation. These results revealed that AcoD with a low zinc ion concentration can effectively increase the removal percentage of ARGs. The results provide guidance for biogas recovery and use of mesophilic AcoD with FW and WAS containing high zinc ion concentrations without pretreatment process.},
}

*Zinc
*Sewage/microbiology
Anaerobiosis
*Bioreactors
*Methane/metabolism
*Drug Resistance, Microbial/genetics
*Microbiota/drug effects
Food
Waste Disposal, Fluid/methods
Food Loss and Waste

@article {pmid39369676,
year = {2024},
author = {Zhuang, Y and Liu, S and Xiao, J and Chen, T and Gao, D and Xu, Y and Jiang, W and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z},
title = {Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136005},
doi = {10.1016/j.jhazmat.2024.136005},
pmid = {39369676},
issn = {1873-3336},
mesh = {Animals ; Cattle ; *Virulence Factors/genetics ; *Metagenomics ; *Feces/microbiology ; *Dairying ; Microbiota ; Female ; Colostrum/microbiology ; Soil Microbiology ; Wastewater/microbiology ; Rumen/microbiology ; },
abstract = {Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.},
}

Animals
Cattle
*Virulence Factors/genetics
*Metagenomics
*Feces/microbiology
*Dairying
Microbiota
Female
Colostrum/microbiology
Soil Microbiology
Wastewater/microbiology
Rumen/microbiology

@article {pmid39362120,
year = {2024},
author = {Gao, S and Li, S and Cao, S and Zhong, H and He, Z},
title = {Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135889},
doi = {10.1016/j.jhazmat.2024.135889},
pmid = {39362120},
issn = {1873-3336},
mesh = {*Iron/metabolism ; *Microbiota/drug effects ; Metallurgy ; Arsenic/metabolism ; Mining ; Copper ; Bacteria/metabolism/genetics ; Metals, Heavy/toxicity ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; },
abstract = {Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.},
}

*Iron/metabolism
*Microbiota/drug effects
Metallurgy
Arsenic/metabolism
Mining
Copper
Bacteria/metabolism/genetics
Metals, Heavy/toxicity
Soil Microbiology
Soil Pollutants/metabolism/toxicity

@article {pmid39357281,
year = {2024},
author = {Zhang, J and Gao, T and Chen, G and Liang, Y and Nie, X and Gu, W and Li, L and Tong, H and Huang, W and Lu, T and Bian, Z and Su, L},
title = {Vinegar-processed Schisandra Chinensis enhanced therapeutic effects on colitis-induced depression through tryptophan metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {135},
number = {},
pages = {156057},
doi = {10.1016/j.phymed.2024.156057},
pmid = {39357281},
issn = {1618-095X},
mesh = {Animals ; *Schisandra/chemistry ; *Depression/drug therapy ; Male ; Mice ; *Tryptophan/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Acetic Acid ; *Colitis, Ulcerative/drug therapy/chemically induced ; *Disease Models, Animal ; Mice, Inbred C57BL ; Blood-Brain Barrier/drug effects ; Dextran Sulfate ; Colon/drug effects/metabolism ; Cytokines/metabolism ; Hippocampus/drug effects/metabolism ; Plant Extracts/pharmacology ; Intestinal Mucosa/drug effects/metabolism ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease characterized by its incurable nature and undefined etiology, which is often accompanied by a high prevalence of comorbid depression. The gut-brain axis has emerged as a promising treatment target in recent years.

PURPOSE: This study aimed to investigate how vinegar-processed Schisandra Chinensis (VSC) enhances therapeutic effects on depressive behavior in chronic UC mice.

METHODS: A chronic UC model was induced in mice using dextran sulfate sodium. The therapeutic effects of both raw and vinegar-processed Schisandra Chinensis on UC and associated depressive symptoms were assessed. Colonic mucosal damage was evaluated using hematoxylin and eosin (H&E) and Alcian blue staining. The integrity of the blood-brain barrier (BBB) and synaptic structures was visualized via transmission electron microscopy (TEM). Enzyme-linked immunosorbent assay (ELISA) was employed to quantify inflammatory cytokine levels in the colon, serum, and brain, while western blotting was performed for protein expression analysis. Additionally, metagenomic analysis was conducted to investigate gut microbiota composition. Nissl staining and immunofluorescence were used to assess hippocampal neuronal damage, and behavioral assessments including the morris water maze, open field test, forced swimming test and tail suspension test, were implemented to evaluate depressive states. Serum metabolites were analyzed using UPLC-MS/MS.

RESULTS: Both raw and vinegar-processed Schisandra Chinensis significantly upregulated aryl hydrocarbon receptor (AhR), inhibited NF-κB p-p65 activation, and reduced levels of pro-inflammatory cytokine. These treatments also enhanced the expression of tight junction proteins, restored colonic mucosal and BBB integrity, alleviated damage to hippocampal neurons, and improved synaptic structure. Behavioral assessments indicated that VSC was particularly effective in ameliorating depressive-like behaviors in chronic UC mice. In the gut, both treatments reshaped the gut microbial composition, restoring the relative abundance of Duncaniella, Candidatus_Amulumruptor, Alistipes, Parabacteroides, Lachnospiraceae_bacterium, uncultured_Bacteroides_sp., Candidatus_Amulumruptor_caecigallinarius, with VSC showing more pronounced effects. Serum metabolomics revealed an increase in tryptophan levels and a decrease in kynurenine and xanthurenic acid levels with VSC, indicating that tryptophan metabolism shifted from the kynurenine pathway to the 5-HT or indole pathway. However, this phenomenon did not occur with Schisandra Chinensis (SC).

CONCLUSION: This study demonstrated that the disruption of tryptophan metabolic balance served as a biological mechanism underlying the occurrence of depressive behaviors induced by UC. The application of SC following vinegar processing enhanced its regulatory effects on gut microbiota and tryptophan metabolism. This findings provided a new insight for the clinical management of gut-brain comorbidities.},
}

Animals
*Schisandra/chemistry
*Depression/drug therapy
Male
Mice
*Tryptophan/pharmacology
*Gastrointestinal Microbiome/drug effects
*Acetic Acid
*Colitis, Ulcerative/drug therapy/chemically induced
*Disease Models, Animal
Mice, Inbred C57BL
Blood-Brain Barrier/drug effects
Dextran Sulfate
Colon/drug effects/metabolism
Cytokines/metabolism
Hippocampus/drug effects/metabolism
Plant Extracts/pharmacology
Intestinal Mucosa/drug effects/metabolism

@article {pmid39305601,
year = {2024},
author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T},
title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135901},
doi = {10.1016/j.jhazmat.2024.135901},
pmid = {39305601},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Fresh Water/microbiology ; Water Pollutants, Chemical/toxicity ; Biofilms/drug effects ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Virulence Factors/genetics ; Polyhydroxyalkanoates ; Polyesters/metabolism ; Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Biodegradable Plastics ; },
abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.},
}

*Microplastics/toxicity
*Drug Resistance, Microbial/genetics
*Fresh Water/microbiology
Water Pollutants, Chemical/toxicity
Biofilms/drug effects
Bacteria/genetics/drug effects
Genes, Bacterial
Virulence Factors/genetics
Polyhydroxyalkanoates
Polyesters/metabolism
Microbiota/drug effects/genetics
Biodegradation, Environmental
Biodegradable Plastics

@article {pmid39299446,
year = {2024},
author = {Wei, ZY and Feng, M and Zhang, DX and Jiang, CY and Deng, Y and Wang, ZJ and Feng, K and Song, Y and Zhou, N and Wang, YL and Liu, SJ},
title = {Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {120029},
doi = {10.1016/j.envres.2024.120029},
pmid = {39299446},
issn = {1096-0953},
mesh = {*Microbiota ; *Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Seasons ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Bacteria/genetics/classification ; Phosphorus/analysis ; },
abstract = {The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.},
}

*Microbiota
*Wastewater/microbiology
Waste Disposal, Fluid/methods
Seasons
RNA, Ribosomal, 16S/genetics
Sewage/microbiology
Bacteria/genetics/classification
Phosphorus/analysis

@article {pmid39298952,
year = {2024},
author = {Liu, J and Shi, J and Hu, Y and Su, Y and Zhang, Y and Wu, X},
title = {Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera).},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135886},
doi = {10.1016/j.jhazmat.2024.135886},
pmid = {39298952},
issn = {1873-3336},
mesh = {Animals ; Bees/drug effects/metabolism ; *Pyrethrins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Insecticides/toxicity ; Catalase/metabolism ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Intestines/drug effects/microbiology ; },
abstract = {Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.},
}

Animals
Bees/drug effects/metabolism
*Pyrethrins/toxicity
*Gastrointestinal Microbiome/drug effects
*Insecticides/toxicity
Catalase/metabolism
Superoxide Dismutase/metabolism
Glutathione Transferase/metabolism
Intestines/drug effects/microbiology

@article {pmid39276741,
year = {2024},
author = {Kumar, A and Lakhawat, SS and Singh, K and Kumar, V and Verma, KS and Dwivedi, UK and Kothari, SL and Malik, N and Sharma, PK},
title = {Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135804},
doi = {10.1016/j.jhazmat.2024.135804},
pmid = {39276741},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Waste Disposal Facilities ; *Biodegradation, Environmental ; *Plastics ; *Bacteria/genetics/classification/metabolism ; *Fungi/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Soil Pollutants/metabolism ; },
abstract = {In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.},
}

*Soil Microbiology
*Waste Disposal Facilities
*Biodegradation, Environmental
*Plastics
*Bacteria/genetics/classification/metabolism
*Fungi/genetics
Metagenomics
RNA, Ribosomal, 16S/genetics
Microbiota
Soil Pollutants/metabolism

@article {pmid39611142,
year = {2024},
author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F},
title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1443468},
pmid = {39611142},
issn = {1664-3224},
mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.

METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.

RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). β diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (≤4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.

CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.},
}

Humans
*Peritonitis/microbiology/etiology/diagnosis
*Peritoneal Dialysis/adverse effects
Male
Female
Middle Aged
Risk Factors
*Gastrointestinal Microbiome
Aged
Risk Assessment
Adult
Metagenomics/methods
High-Throughput Nucleotide Sequencing

@article {pmid39611041,
year = {2024},
author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae378},
pmid = {39611041},
issn = {2053-714X},
abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.},
}

@article {pmid39609882,
year = {2024},
author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M},
title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {249},
pmid = {39609882},
issn = {2049-2618},
mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; },
abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.

RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.

CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.},
}

*Archaea/classification/genetics/metabolism
*Lakes/microbiology
*Phylogeny
*Ecotype
Ecosystem
Metagenomics
Microbiota
Genome, Archaeal
Water Microbiology
Biodiversity

@article {pmid39609616,
year = {2024},
author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS},
title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1590},
pmid = {39609616},
issn = {2399-3642},
support = {R21 AI175965/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; },
abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.},
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Sputum/microbiology
*Cystic Fibrosis/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Freezing
Adult
Cryopreservation
Female
High-Throughput Nucleotide Sequencing/methods
Bacteria/genetics/isolation & purification/classification
Sequence Analysis, DNA/methods
Male
Respiratory System/microbiology

@article {pmid39608999,
year = {2024},
author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL},
title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.},
journal = {BMJ open},
volume = {14},
number = {11},
pages = {e078660},
doi = {10.1136/bmjopen-2023-078660},
pmid = {39608999},
issn = {2044-6055},
mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; },
abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.

METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.

ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.

TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.},
}

Humans
*Alzheimer Disease/drug therapy/genetics
Philippines
Prospective Studies
Aged
Cholinesterase Inhibitors/therapeutic use
Rivastigmine/therapeutic use
Donepezil/therapeutic use
Cross-Sectional Studies
Memantine/therapeutic use
Male
Female
Metabolomics
Gastrointestinal Microbiome/drug effects
Multiomics

@article {pmid39030898,
year = {2024},
author = {Stevens, C and Norris, S and Arbeeva, L and Carter, S and Enomoto, M and Nelson, AE and Lascelles, BDX},
title = {Gut Microbiome and Osteoarthritis: Insights From the Naturally Occurring Canine Model of Osteoarthritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {76},
number = {12},
pages = {1758-1763},
doi = {10.1002/art.42956},
pmid = {39030898},
issn = {2326-5205},
mesh = {Dogs ; Animals ; *Gastrointestinal Microbiome ; *Osteoarthritis/microbiology ; *Disease Models, Animal ; *Feces/microbiology ; Male ; Female ; Firmicutes/isolation & purification ; Pain/microbiology ; Metagenomics ; },
abstract = {OBJECTIVE: The purpose of this study was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.

METHODS: Fecal samples were collected from 93 owned pet dogs. Dogs were designated as either clinically healthy or OA pain using validated methods. Metagenomic profiling was performed through shotgun sequencing using the Illumina NovaSeq platform. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance. Comparisons between healthy and OA-pain groups were performed individually for each taxa using nonparametric tests following Benjamini and Hochberg adjustment for multiple comparisons. Permutation analysis of variance was performed using Bray-Curtis distance matrices. All downstream analyses were completed in R.

RESULTS: No significant differences between healthy and OA-pain dogs were observed for alpha and beta diversity. We found 13 taxa with nominally significant (P < 0.05) associations with OA case status, but none of the associations remained significant after adjustment for multiple comparisons. No differences in alpha or beta diversities or the Firmicutes to Bacteroidetes ratio were found regarding pain severity, mobility or activity level, age, or body composition score.

CONCLUSION: Similar to recent studies in humans, the present study did not demonstrate a significant difference in the fecal microbial communities between dogs with OA pain and healthy control dogs. Future research in this naturally occurring model should expand on these data and relate the gut microbiome to gut permeability and circulating proinflammatory and anti-inflammatory molecules to better understand the influence of the gut microbiome on OA and OA pain.},
}

Dogs
Animals
*Gastrointestinal Microbiome
*Osteoarthritis/microbiology
*Disease Models, Animal
*Feces/microbiology
Male
Female
Firmicutes/isolation & purification
Pain/microbiology
Metagenomics

@article {pmid39607975,
year = {2024},
author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI},
title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.},
journal = {Parasite (Paris, France)},
volume = {31},
number = {},
pages = {74},
doi = {10.1051/parasite/2024074},
pmid = {39607975},
issn = {1776-1042},
support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; },
mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.},
}

Animals
*Rhipicephalus/microbiology
*RNA, Ribosomal, 16S/genetics
*Ixodidae/microbiology
*Microbiota
Pakistan
Phylogeny
Symbiosis
Female
Gastrointestinal Microbiome
Coxiella/genetics/isolation & purification/classification
Bacteria/classification/genetics/isolation & purification

@article {pmid39604824,
year = {2024},
author = {Li, X and Zhang, Z and Bai, H and Liu, Z},
title = {Analysis of vaginal microbiota during postpartum and postmenopausal periods based on metagenomics.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {501},
pmid = {39604824},
issn = {1471-2180},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Postmenopause ; *Postpartum Period ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Postmenopausal and the postpartum periods are essential physiological phases that result in low estrogen levels in women; however, they are important to female reproductive health. Traditional as well as new detection methods (such as 16 S RNA sequencing) have limitations in detecting the composition of vaginal microbiota. Therefore, in this study, we used metagenomic detection technology to study the composition of vaginal microbiota in postmenopausal and postpartum women. Six women were randomly selected from each group (healthy women of childbearing age, postmenopausal group, and postpartum) for vaginal microecology, composition, α-diversity, linear discriminant analysis effect size (LEfSe), and Comprehensive Antibiotic Resistance Database (CARD) analyses.

RESULTS: We discovered that Lactobacillus dominance disappeared in postpartum and postmenopausal group women and that diversity increased. However, the proportions of Atopobium vaginae, Escherichia coli, and Streptococcus agalactiae significantly increased. Diversity was the highest in the postpartum period, with a significant increase in the proportions of A. vaginae, Gardnerella vaginalis, Prevotella, and occasionally, Chlamydia trachomatis. Linear discriminant analysis effect size analysis revealed that Lactobacillus crispatus and L. iners enrichment in the postpartum and menopausal periods was much lower than that in the childbearing age group. CARD analysis revealed that ABC-F ATP-binding cassette ribosomal protection protein subfamily gene abundance was significantly lower in the menopausal than in the childbearing age group, whereas the gimA family macrolide glycosyltransferase gene abundance was significantly higher.

CONCLUSIONS: The dominance of vaginal Lactobacillus in postpartum and menopausal women disappeared, while their diversity increased. In addition, the reproductive tract of postpartum women was susceptible to invasion by pathogenic microorganisms, which deserves clinical attention. When menopausal women receive treatment for vaginal infections, the likelihood that certain bacterial communities develop antibiotic resistance through ribosomal protection mechanisms is lower than that of women in the childbearing age, while the possibility of developing resistance to macrolides through glycosylation may increase. This, however, requires further research.},
}

Humans
Female
*Vagina/microbiology
*Postmenopause
*Postpartum Period
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Adult
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid39604394,
year = {2024},
author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N},
title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10291},
pmid = {39604394},
issn = {2041-1723},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; },
abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.},
}

Humans
*Colitis, Ulcerative/microbiology/genetics/virology
*Crohn Disease/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
Male
*Metagenomics/methods
Female
*Bacteriophages/genetics
Adult
Escherichia coli/genetics/metabolism
Middle Aged
Japan
Fungi/genetics
Bacteria/genetics/metabolism/classification
Metagenome/genetics
Saccharomyces cerevisiae/genetics
Bifidobacterium/genetics
Virome/genetics
Enterococcus faecium/genetics/pathogenicity
Fatty Acids, Volatile/metabolism
Young Adult
China
Case-Control Studies

@article {pmid39572788,
year = {2024},
author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Szamosvári, D and Imminger, S and Seki, D and Shazzad, JB and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Böttcher, T and Cheng, JX and Wagner, M},
title = {The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3165-3183},
pmid = {39572788},
issn = {2058-5276},
support = {10.55776; COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; ZK-57//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; Z383-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776 COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; R01EB032391//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM136223//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI141439//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Iron/metabolism ; *Parkinson Disease/microbiology/metabolism/drug therapy ; *Feces/microbiology ; *Catechols/pharmacology/metabolism ; *Nitriles/pharmacology ; Homeostasis/drug effects ; Bacteria/genetics/drug effects/metabolism/classification/isolation & purification ; Metagenomics ; Antiparkinson Agents/pharmacology ; },
abstract = {Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson's disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Iron/metabolism
*Parkinson Disease/microbiology/metabolism/drug therapy
*Feces/microbiology
*Catechols/pharmacology/metabolism
*Nitriles/pharmacology
Homeostasis/drug effects
Bacteria/genetics/drug effects/metabolism/classification/isolation & purification
Metagenomics
Antiparkinson Agents/pharmacology

@article {pmid39567665,
year = {2024},
author = {Zhang, T and Hasegawa, Y and Waldor, MK},
title = {Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3376-3390},
pmid = {39567665},
issn = {2058-5276},
support = {MKW//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {Animals ; Mice ; *Homeostasis ; *Citrobacter rodentium ; *Enterobacteriaceae Infections/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Bile/metabolism ; Liver/metabolism/microbiology ; Listeria monocytogenes/genetics ; Mice, Inbred C57BL ; Intestines/microbiology ; Metabolomics ; Listeriosis/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Specific Pathogen-Free Organisms ; },
abstract = {The liver makes bile, an aqueous solution critical for fat absorption, which is secreted into the duodenum. Despite extensive studies on bile salts, other components of bile are less well characterized. Here we used global metabolomic analysis on bile from specific-pathogen-free, germ-free, Citrobacter rodentium-infected or Listeria monocytogenes-infected mice and identified a metabolome of 812 metabolites that were altered by both microbiota and enteric infection. Hepatic transcriptomics identified enteric-infection-triggered pathways that probably underlie bile remodelling. Enteric infection increased levels of four dicarboxylates in bile, including itaconate. Analysis of Acod1[-/-] mice indicated that increased itaconate also increased tuft cell abundance, altered microbiota composition and function as detected by metagenomic analysis, and modulated host defence, leading to reduced Vibrio cholerae colonization. Our data suggest that enteric-infection-associated signals are relayed between the intestine and liver and induce transcriptional programmes that shape the bile metabolome, modifying the immunomodulatory and host defence functions of bile.},
}

Animals
Mice
*Homeostasis
*Citrobacter rodentium
*Enterobacteriaceae Infections/microbiology/metabolism
*Metabolome
*Gastrointestinal Microbiome
*Bile/metabolism
Liver/metabolism/microbiology
Listeria monocytogenes/genetics
Mice, Inbred C57BL
Intestines/microbiology
Metabolomics
Listeriosis/microbiology/metabolism
Bile Acids and Salts/metabolism
Specific Pathogen-Free Organisms

@article {pmid39448846,
year = {2024},
author = {Wu, Z and Liu, S and Ni, J},
title = {Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3362-3375},
pmid = {39448846},
issn = {2058-5276},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92047303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 423B2703//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/genetics/virology ; *Metagenomics ; *Interspersed Repetitive Sequences ; *Archaeal Viruses/genetics/classification ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Phylogeny ; Metagenome ; Genome, Viral/genetics ; Genome, Archaeal ; Virome/genetics ; Symbiosis ; },
abstract = {The archaeal superphylum DPANN (an acronym formed from the initials of the first five phyla discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota and Nanoarchaeota) is a group of ultrasmall symbionts able to survive in extreme ecosystems. The diversity and dynamics between DPANN archaea and their virome remain largely unknown. Here we use a metagenomic clustered regularly interspaced short palindromic repeats (CRISPR) screening approach to identify 97 globally distributed, non-redundant viruses and unclassified mobile genetic elements predicted to infect hosts across 8 DPANN phyla, including 7 viral groups not previously characterized. Genomic analysis suggests a diversity of viral morphologies including head-tailed, tailless icosahedral and spindle-shaped viruses with the potential to establish lytic, chronic or lysogenic infections. We also find evidence of a virally encoded Cas12f1 protein (probably originating from uncultured DPANN archaea) and a mini-CRISPR array, which could play a role in modulating host metabolism. Many metagenomes have virus-to-host ratios >10, indicating that DPANN viruses play an important role in controlling host populations. Overall, our study illuminates the underexplored diversity, functional repertoires and host interactions of the DPANN virome.},
}

*Archaea/genetics/virology
*Metagenomics
*Interspersed Repetitive Sequences
*Archaeal Viruses/genetics/classification
*Clustered Regularly Interspaced Short Palindromic Repeats
Phylogeny
Metagenome
Genome, Viral/genetics
Genome, Archaeal
Virome/genetics
Symbiosis

@article {pmid38349437,
year = {2024},
author = {Gu, L and Alemasi, A and Chen, Y and Li, X and Mei, Y and Zhou, J and He, D and Zeng, J},
title = {Gut Microbiota Disorders in Obesity-Associated Benign Prostatic Hyperplasia in Rats.},
journal = {Biochemical genetics},
volume = {62},
number = {6},
pages = {4639-4653},
pmid = {38349437},
issn = {1573-4927},
support = {82172684//National Natural Science Foundation of China/ ; 82073304//National Natural Science Foundation of China/ ; 2019YFC0121501//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Male ; *Prostatic Hyperplasia/microbiology/pathology ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; *Rats, Sprague-Dawley ; Rats ; *Diet, High-Fat/adverse effects ; Prostate/microbiology/pathology/metabolism ; },
abstract = {UNLABELLED: Benign prostatic hyperplasia (BPH), commonly seen in older men, can cause symptoms of discomfort, and may even need surgical intervention. Studies have shown the potential link between gut microbes and BPH, but the molecular association is not fully understood.

METHODS: Four-week-old male Sprague-Dawley rats (n = 16) were randomly allocated to normal control diet (ND, 10% fat) and high-fat diet-induced BPH (HFD, 45% fat) groups. Metagenomic analysis was used to examine the abundance and discrepancies in gut microbiota within the two groups after 24 weeks of feeding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted to assess the biological functions of the differentially expressed genes.

RESULTS: Rats with HFD-induced obesity exhibited morphological abnormalities in their prostate tissues. Metagenomic analysis of the gut revealed that Firmicutes were the dominant phyla in the HFD group, whereas the ND group had a higher abundance of Spirochaetes. At the genus level, Ruminococcus spp exhibited greater abundance in the HFD group, whereas Treponema spp were more abundant in the ND group. KEGG analysis demonstrated that the differentially expressed genes were mainly enriched in the NOD-like receptor (NLR) signaling, PI3K-Akt signaling, estrogen-signaling, signalings associated with GABAergic synapses, pantothenate and CoA biosynthesis.

CONCLUSION: The findings of our study indicated that there was a notable variation in the microbiota abundance within the intestinal tract of obese rats suffering from prostate hyperplasia. It is plausible that these differentially abundant bacteria played a role in the development of pathological alterations in the prostate through the facilitation of inflammatory responses; however, additional research is required to validate the findings.},
}

Animals
Male
*Prostatic Hyperplasia/microbiology/pathology
*Gastrointestinal Microbiome
*Obesity/microbiology
*Rats, Sprague-Dawley
Rats
*Diet, High-Fat/adverse effects
Prostate/microbiology/pathology/metabolism

@article {pmid38285123,
year = {2024},
author = {Rana, S and Singh, P and Bhardwaj, T and Somvanshi, P},
title = {A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach.},
journal = {Biochemical genetics},
volume = {62},
number = {6},
pages = {4264-4279},
pmid = {38285123},
issn = {1573-4927},
mesh = {*Asthma/microbiology/genetics ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; Gastrointestinal Microbiome ; Female ; Metabolic Networks and Pathways ; Male ; Adult ; },
abstract = {Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.},
}

*Asthma/microbiology/genetics
Humans
*Metagenome
RNA, Ribosomal, 16S/genetics
Computer Simulation
Gastrointestinal Microbiome
Female
Metabolic Networks and Pathways
Male
Adult

@article {pmid39603713,
year = {2024},
author = {Helfrich, PG and Feldman, J and Andrade-Barahona, E and Robertson, I and Foster, J and Hofacker, R and Dahlquist Selking, G and Sheik, CS and Cox, A},
title = {Aqueous copper geochemistry shapes the sediment microbial resistome in a recovering stream.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70045},
doi = {10.1111/1758-2229.70045},
pmid = {39603713},
issn = {1758-2229},
support = {800015-10297//Montana Department of Justice, Natural Resource Damage Program (NRDP) through the Butte Natural Resource Damage Restoration Council (BNRC)/ ; //Montana Tech Faculty Seed and Faculty Development Initiatives/ ; //Montana Tech Earth Science and Engineering Fellowship/ ; //Montana Water Center, Faculty Seed Grant/ ; },
mesh = {*Copper/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/metabolism/isolation & purification ; Metagenome ; Water Pollutants, Chemical/metabolism ; Metagenomics ; Arsenic/metabolism ; Microbiota/genetics/drug effects ; },
abstract = {Aqueous metals are pervasive contaminants associated with historical mining. We produced and examined 16 metagenomes from a contaminated creek to investigate how anthropogenic metal contamination shapes the functional profiles of microbial communities. We then incorporated the metagenomic profiles and concurrently collected geochemical context into a multivariate model to examine correlations between stream geochemistry and microbial functional potential. Integrating the metagenomes with full geochemical profiles emphasised that even low metalloid concentrations shaped microbial functionality, seasonal shifts in copper bioavailability and arsenic exposure correlated with genetic variation, and copper resistomes were spatiotemporally distinct. This study provides new insights into microbial metabolic potential and microbe-metal(loid) interactions.},
}

*Copper/metabolism
*Geologic Sediments/microbiology/chemistry
*Rivers/microbiology/chemistry
*Bacteria/genetics/drug effects/classification/metabolism/isolation & purification
Metagenome
Water Pollutants, Chemical/metabolism
Metagenomics
Arsenic/metabolism
Microbiota/genetics/drug effects

@article {pmid39601988,
year = {2024},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1265},
pmid = {39601988},
issn = {1573-2959},
mesh = {*Bacteria/classification/isolation & purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.},
}

*Bacteria/classification/isolation & purification/genetics
*Petroleum Pollution
*Environmental Monitoring
India
*Soil Microbiology
Biodiversity
Bays/microbiology
Drug Resistance, Bacterial

@article {pmid39601293,
year = {2024},
author = {Liu, L and Cao, S and Lin, W and Gao, Z and Yang, L and Zhu, L and Yang, B and Zhang, G and Zhu, R and Wu, D},
title = {miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2434029},
doi = {10.1080/19490976.2024.2434029},
pmid = {39601293},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; Gastrointestinal Microbiome ; Software ; Case-Control Studies ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Propensity Score ; },
abstract = {Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.},
}

*Metagenomics/methods
Humans
Gastrointestinal Microbiome
Software
Case-Control Studies
Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome
Propensity Score

@article {pmid39599783,
year = {2024},
author = {Vila-Nistal, M and Logares, R and Gasol, JM and Martinez-Garcia, M},
title = {Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/v16111669},
pmid = {39599783},
issn = {1999-4915},
support = {PID2021-125175OB-I00//Agencia Estatal de Investigación/ ; CTM2015-70340-R//Agencia Estatal de Investigación/ ; RTI2018-101025-B-I00//Agencia Estatal de Investigación/ ; },
mesh = {*Seawater/virology ; *Metagenomics/methods ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Aquatic Organisms/virology ; Virome/genetics ; },
abstract = {Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10[3] copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.},
}

*Seawater/virology
*Metagenomics/methods
Genome, Viral
Phylogeny
Evolution, Molecular
Aquatic Organisms/virology
Virome/genetics

@article {pmid39599719,
year = {2024},
author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K},
title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
doi = {10.3390/nu16223933},
pmid = {39599719},
issn = {2072-6643},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; Thailand ; Female ; Young Adult ; *Healthy Volunteers ; *Feces/microbiology ; Middle Aged ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Dietary Sugars ; Southeast Asian People ; },
abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.

METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.

RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.

CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.},
}

Humans
*Gastrointestinal Microbiome
Adult
Male
Thailand
Female
Young Adult
*Healthy Volunteers
*Feces/microbiology
Middle Aged
Adolescent
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
Dietary Sugars
Southeast Asian People

@article {pmid39598209,
year = {2024},
author = {Al-Awthan, YS and Mir, R and Alharbi, BM and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alatawi, MM},
title = {Metagenomic Analysis of Sediment Bacterial Diversity and Composition in Natural Lakes and Artificial Waterpoints of Tabuk Region in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/life14111411},
pmid = {39598209},
issn = {2075-1729},
abstract = {The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km[2] between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km[2]. It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve's natural ecosystems.},
}

@article {pmid39597714,
year = {2024},
author = {Yang, T and He, Y and Yang, M and Gao, Z and Zhou, J and Wang, Y},
title = {Community Structure and Biodiversity of Active Microbes in the Deep South China Sea.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112325},
pmid = {39597714},
issn = {2076-2607},
support = {42376149//National Natural Science Foundation of China/ ; },
abstract = {The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean.},
}

@article {pmid39597627,
year = {2024},
author = {Vilo, C and Fábrega, F and Campos, VL and Gómez-Silva, B},
title = {Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112238},
pmid = {39597627},
issn = {2076-2607},
support = {FB 0001//ANID, Chile/ ; },
abstract = {The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.},
}

@article {pmid39596262,
year = {2024},
author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P},
title = {Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut-Liver Axis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212196},
pmid = {39596262},
issn = {1422-0067},
support = {32302976//National Natural Science Foundation of China/ ; BK20230179//Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; },
mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism ; Nutritive Value ; Lipid Metabolism ; Fishes/metabolism/growth & development ; Animal Feed ; Glycolipids/metabolism ; },
abstract = {Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 10[8] CFU/g) (PF) and water (1.0 × 10[8] CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota-gut-liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut-liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.},
}

*Probiotics/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Liver/metabolism
Nutritive Value
Lipid Metabolism
Fishes/metabolism/growth & development
Animal Feed
Glycolipids/metabolism

@article {pmid39593380,
year = {2024},
author = {Cardinali, F and Rampanti, G and Paderni, G and Milanović, V and Ferrocino, I and Reale, A and Boscaino, F and Raicevic, N and Ilincic, M and Osimani, A and Aquilanti, L and Martinovic, A and Garofalo, C},
title = {A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115169},
doi = {10.1016/j.foodres.2024.115169},
pmid = {39593380},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Food Microbiology ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Biogenic Amines/analysis ; Montenegro ; Bacteria/classification ; Odorants/analysis ; },
abstract = {The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g[-1]). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.},
}

*Cheese/microbiology/analysis
*Food Microbiology
*Microbiota
*Volatile Organic Compounds/analysis
*Biogenic Amines/analysis
Montenegro
Bacteria/classification
Odorants/analysis

@article {pmid39593354,
year = {2024},
author = {Peng, Q and Zheng, H and Zhou, H and Chen, J and Xu, Y and Wang, Z and Xie, G},
title = {Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115139},
doi = {10.1016/j.foodres.2024.115139},
pmid = {39593354},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis ; *Fermentation ; *Microbiota ; *Wine/analysis/microbiology ; *Taste ; Humans ; Gas Chromatography-Mass Spectrometry ; Solid Phase Microextraction ; Pentanols/metabolism/analysis ; Odorants/analysis ; Flavoring Agents/analysis ; China ; Male ; Saccharomyces cerevisiae/metabolism ; Food Microbiology ; Female ; Phenylethyl Alcohol/metabolism/analysis ; Adult ; Butanols ; },
abstract = {Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC-MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu's core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.},
}

*Volatile Organic Compounds/analysis
*Fermentation
*Microbiota
*Wine/analysis/microbiology
*Taste
Humans
Gas Chromatography-Mass Spectrometry
Solid Phase Microextraction
Pentanols/metabolism/analysis
Odorants/analysis
Flavoring Agents/analysis
China
Male
Saccharomyces cerevisiae/metabolism
Food Microbiology
Female
Phenylethyl Alcohol/metabolism/analysis
Adult
Butanols

@article {pmid39593339,
year = {2024},
author = {Scarano, L and Peruzy, MF and Fallico, V and Blaiotta, G and Aponte, M and Anastasio, A and Murru, N},
title = {Provolone del Monaco PDO cheese: Lactic microflora, biogenic amines and volatilome characterization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115257},
doi = {10.1016/j.foodres.2024.115257},
pmid = {39593339},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Biogenic Amines/analysis/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteriocins ; Tyramine/analysis/metabolism ; Lactobacillales/metabolism/genetics/isolation & purification ; },
abstract = {One commercial production run of Provolone del Monaco - a long-ripened pasta filata cheese - was followed up to the end of ripening for a total of 20 samples. 371 LAB isolates were subject to genetic characterization followed by 16S rRNA gene sequencing. The dominant species were Lacticaseibacillus casei/paracasei (19.4 %), Streptococcus macedonicus (19.1 %) and Enterococcus faecalis (13.2 %). Strains were screened for features of technological interest or safety relevance. Tyramine-producing cultures were quite common, above all within enterococci. By MALDI TOF Mass Spectrometry, one Lactococcus lactis and one Enterococcus faecium strain proved to be bacteriocin producers. Four further cheese wheels from the same production run at 623 days of ripening were evaluated for volatile organic compounds, biogenic amines, and bacterial community by metagenomic sequencing. Three individual wheel samples shared a rather similar microbiome with Lactobacillus delbrueckii and Streptococcus thermophilus as the most represented species, while the fourth wheel appeared wholly different being dominated by Lentilactobacillus buchneri and St. infantarius. Additionally, this sample had the greatest content of biogenic amines and a different VOCs composition. Given the variance seen among cheese wheels processed and ripened under the same conditions, the search for adjunct cultures in the production of this cheese seems to be of utmost importance.},
}

*Cheese/microbiology/analysis
*Biogenic Amines/analysis/metabolism
*Volatile Organic Compounds/analysis/metabolism
*Food Microbiology
RNA, Ribosomal, 16S/genetics
Microbiota
Bacteriocins
Tyramine/analysis/metabolism
Lactobacillales/metabolism/genetics/isolation & purification

@article {pmid39593310,
year = {2024},
author = {Li, X and Du, C and Zhao, Y and Li, J and Hu, Y and Dong, W and Peng, N and Zhao, S},
title = {Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115224},
doi = {10.1016/j.foodres.2024.115224},
pmid = {39593310},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Food Microbiology ; *Taste ; Ethanol/metabolism ; Fermented Foods/microbiology ; Lactobacillales/genetics/metabolism/classification ; Lactic Acid/metabolism/analysis ; Fungi/classification/genetics ; Acetic Acid/metabolism/analysis ; Oryza/microbiology ; Bacteria/classification/genetics/metabolism ; Flavoring Agents/analysis ; },
abstract = {Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.},
}

*Fermentation
*Microbiota
*Food Microbiology
*Taste
Ethanol/metabolism
Fermented Foods/microbiology
Lactobacillales/genetics/metabolism/classification
Lactic Acid/metabolism/analysis
Fungi/classification/genetics
Acetic Acid/metabolism/analysis
Oryza/microbiology
Bacteria/classification/genetics/metabolism
Flavoring Agents/analysis

@article {pmid39545702,
year = {2024},
author = {Zhang, M and Ma, L and Luo, J and Ren, T and Liu, S and Pan, L and Bao, Y and Li, F and Dai, Y and Pi, Z and Yue, H and Zheng, F},
title = {Low-Medium Polarity Ginsenosides from Wild Ginseng Improves Immunity by Activating the AhR/MAPK Pathway through Tryptophan Metabolism Driven by Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {47},
pages = {26142-26154},
doi = {10.1021/acs.jafc.4c06019},
pmid = {39545702},
issn = {1520-5118},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Panax/chemistry ; Mice ; *Tryptophan/metabolism ; *Ginsenosides/pharmacology/administration & dosage ; *Plant Extracts/pharmacology/administration & dosage ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; Humans ; Immunity/drug effects ; MAP Kinase Signaling System/drug effects ; Spleen/drug effects/metabolism/immunology ; Intestinal Mucosa/metabolism/immunology/drug effects ; Mice, Inbred BALB C ; },
abstract = {The gut microbiota contribute significantly to the immune system. Low-medium polarity ginsenosides from wild ginseng (LWG) have potential immunomodulatory effects. However, how the LWG regulates gut microbiota to enhance immunity remains unclear. To explore the interaction between gut microbes and metabolites mediating LWG's immunomodulatory effects, this study examined LWG's impact on splenocytes and CTX-induced immunosuppressed mice. Metabolomic and metagenomic analyses were conducted in vivo to explore the mechanism by which LWG regulates gut microbiota to enhance immunity. In vitro data suggest that LWG at 4 μg/mL enhances the splenocyte activity. Furthermore, LWG effectively reduces symptoms in immunocompromised mice, including weight loss and intestinal mucosal damage. LWG alleviated gut microbiota disturbance, restored tryptophan metabolites (IA, IAA, and IPA), and significantly increased JNK, ERK, and p38MAPK protein levels, which were downstream of AhR. Our study demonstrated that LWG improves the immunity by reshaping gut microbiota, restoring intestinal mucosa, and boosting the gut microbiota-related metabolism of tryptophan to activate the AhR/MAPK pathway. This research offers new insights into the mechanism by which LWG regulates immune function.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Panax/chemistry
Mice
*Tryptophan/metabolism
*Ginsenosides/pharmacology/administration & dosage
*Plant Extracts/pharmacology/administration & dosage
*Receptors, Aryl Hydrocarbon/metabolism/genetics
Male
Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
Humans
Immunity/drug effects
MAP Kinase Signaling System/drug effects
Spleen/drug effects/metabolism/immunology
Intestinal Mucosa/metabolism/immunology/drug effects
Mice, Inbred BALB C

@article {pmid39541817,
year = {2024},
author = {Czatzkowska, M and Wolak, I and Harnisz, M and Korzeniewska, E},
title = {Microbial diversity and biosafety judgment of digestates derived from different biogas plants for agricultural applications.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123329},
doi = {10.1016/j.jenvman.2024.123329},
pmid = {39541817},
issn = {1095-8630},
mesh = {*Biofuels ; *Agriculture ; *Soil Microbiology ; Microbiota ; Biodegradation, Environmental ; Anaerobiosis ; Soil/chemistry ; Bacteria/classification ; },
abstract = {The composition of microbial communities is the key to effective anaerobic digestion (AD). The microbiome driving the AD process has been extensively researched, whereas the influence of specific substrates on the microbiome of digestate remains insufficiently investigated. Digestate has considerable potential for use in soil fertilization and bioremediation, therefore its biological safety should be monitored. Moreover, the knowledge about the composition of microbial communities and their interconnections in digestate should be extended, due to the impact on soil microbiota and its functionality. The aim of this study was a comprehensive assessment of the (1) sanitary quality, (2) core microbiome, and (3) microbial interactions in digestates collected from three full-scale agricultural biogas plants, with particular emphasis on their applicability from the perspective of the resident microbiota. Analyzed samples of digestate were derived from various substrates used for AD, including plant- and animal-based materials, and industrial waste. The study demonstrated that the phyla Bacillota, Bacteroidota, and Cloacimonadota were the most dominant in digestates regardless of the composition of the processed substrates, however, member composition at the genus level differed significantly between samples. In addition, we observed that microbial genera belonging to the less prevalent phyla play an integral role in the forming of microbial community interactions. Dominant microbial taxa with broad metabolic capabilities, potentially improving soil quality and functionality, have been identified. Moreover, we confirmed, that digestate samples were free of analyzed pathogenic bacteria and parasites. The study results indicate that digestate may have an immense fertilizing and bioremediation potential that has not been fully availed of to date.},
}

*Biofuels
*Agriculture
*Soil Microbiology
Microbiota
Biodegradation, Environmental
Anaerobiosis
Soil/chemistry
Bacteria/classification

@article {pmid39537082,
year = {2024},
author = {Chettri, D and Verma, AK and Chirania, M and Verma, AK},
title = {Metagenomic approaches in bioremediation of environmental pollutants.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {363},
number = {Pt 2},
pages = {125297},
doi = {10.1016/j.envpol.2024.125297},
pmid = {39537082},
issn = {1873-6424},
mesh = {*Biodegradation, Environmental ; *Metagenomics/methods ; *Environmental Pollutants/metabolism ; Artificial Intelligence ; Microbiota ; },
abstract = {Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.},
}

*Biodegradation, Environmental
*Metagenomics/methods
*Environmental Pollutants/metabolism
Artificial Intelligence
Microbiota

@article {pmid39503092,
year = {2025},
author = {Wu, Y and You, Y and Wu, L and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J},
title = {Integrated metagenomics and metatranscriptomics analyses reveal the impacts of different Lactiplantibacillus plantarum strains on microbial communities and metabolic profiles in pickled bamboo shoots.},
journal = {Food chemistry},
volume = {464},
number = {Pt 2},
pages = {141772},
doi = {10.1016/j.foodchem.2024.141772},
pmid = {39503092},
issn = {1873-7072},
mesh = {*Fermentation ; *Metagenomics ; *Lactobacillus plantarum/metabolism/genetics ; *Microbiota ; Plant Shoots/metabolism/chemistry/microbiology ; Metabolome ; Sasa/microbiology/metabolism ; },
abstract = {Effects of two different Lactobacillus plantarum fermentation processes on microbial communities and metabolic functions were evaluated using metagenomics and metatranscriptomics. Dominant species in Lactobacillus plantarum DACN4208 (LPIF8) and DACN4120 (LPIF10) were Lactobacillus pentosus and Lactobacillus plantarum, with Lactiplantibacillus comprised 75.31 % of the microbial community in LPIF10. Metatranscriptomic revealed that LPIF8 had more genes associated with carbohydrate-binding modules and auxiliary activities, totaling 7500 and 4000 genes, respectively. Metabolic reconstruction further showed that LPIF8 had the most genes involved in pyruvate and lactose metabolism, with 633 and 389 genes, respectively. In contrast, LPIF10 fewer genes related to the biosynthesis and metabolism of phenylalanine, tyrosine, and tryptophan. These results indicate that LPIF8 could efficiently improve fermentation efficiency and increase metabolic activity, while LPIF10 exhibited a more moderate and controlled metabolic process. These provide valuable insights into how different starter cultures influence the structure and metabolic functions of microbial communities in pickled bamboo shoots.},
}

*Fermentation
*Metagenomics
*Lactobacillus plantarum/metabolism/genetics
*Microbiota
Plant Shoots/metabolism/chemistry/microbiology
Metabolome
Sasa/microbiology/metabolism

@article {pmid39393228,
year = {2024},
author = {Dey, G and Maity, JP and Banerjee, P and Sharma, RK and Das, K and Gnanachandrasamy, G and Wang, CW and Lin, PY and Wang, SL and Chen, CY},
title = {Evaluation and mitigation of potentially toxic elements contamination in mangrove ecosystem: Insights into phytoremediation and microbial perspective.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt A},
pages = {117035},
doi = {10.1016/j.marpolbul.2024.117035},
pmid = {39393228},
issn = {1879-3363},
mesh = {*Biodegradation, Environmental ; *Wetlands ; *Water Pollutants, Chemical/analysis ; Taiwan ; Avicennia ; Environmental Monitoring ; Geologic Sediments/chemistry/microbiology ; Microbiota ; Ecosystem ; },
abstract = {Mangroves, essential coastal ecosystems, are threatened by human-induced Potentially-toxic-elements (PTEs) pollution. This study analyzed PTEs distribution, phytoremediation potential, and rhizosphere microbial communities in Taiwan's Xinfeng mangrove forest. Significant variations in physicochemical and PTEs concentrations were observed across adjacent water bodies, with moderate contamination in the river, estuary, and overlying water of mangroves sediment. The partition-coefficient showed the mobility of Bi, Pb, Co, and Sr at the water-sediment interface. The geochemical-indices revealed high Bi and Pb contamination and moderate Zn, Sr, Cu, and Cd contamination in sediment. The overall pollution indices indicated the significant contamination, while moderate ecological risk was found for Cd (40 ≤ Er[i] < 80). Mangroves Kandelia obovata and Avicennia marina exhibited promising PTEs phytoremediation potential (Bi, Cd, Mn, Sr, and Co). Metagenomics indicated a diverse microbial community with N-fixation, P-solubilization, IAA synthesis, and PTEs-resistance genes. These findings underscore the need for targeted conservation to protect these critical habitats.},
}

*Biodegradation, Environmental
*Wetlands
*Water Pollutants, Chemical/analysis
Taiwan
Avicennia
Environmental Monitoring
Geologic Sediments/chemistry/microbiology
Microbiota
Ecosystem

@article {pmid39353343,
year = {2024},
author = {Zheng, X and Li, J and Ouyang, Y and Wu, G and He, X and Wang, D and Zhang, XX},
title = {Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes.},
journal = {Water research},
volume = {267},
number = {},
pages = {122491},
doi = {10.1016/j.watres.2024.122491},
pmid = {39353343},
issn = {1879-2448},
mesh = {*Benzothiazoles ; *Biodegradation, Environmental ; Microbial Consortia ; Rhodococcus/genetics/metabolism ; },
abstract = {The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.},
}

*Benzothiazoles
*Biodegradation, Environmental
Microbial Consortia
Rhodococcus/genetics/metabolism

@article {pmid39592704,
year = {2024},
author = {Hai, C and Hao, Z and Bu, L and Lei, J and Liu, X and Zhao, Y and Bai, C and Su, G and Yang, L and Li, G},
title = {Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1575},
pmid = {39592704},
issn = {2399-3642},
support = {32360837, 32341052//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle ; *Myostatin/genetics/metabolism ; *Amino Acids, Branched-Chain/metabolism/biosynthesis ; *Prevotella/genetics/metabolism ; *Muscle, Skeletal/metabolism ; *Rumen/microbiology/metabolism ; Gene Knockout Techniques ; Gastrointestinal Microbiome/genetics ; },
abstract = {Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.},
}

Animals
Cattle
*Myostatin/genetics/metabolism
*Amino Acids, Branched-Chain/metabolism/biosynthesis
*Prevotella/genetics/metabolism
*Muscle, Skeletal/metabolism
*Rumen/microbiology/metabolism
Gene Knockout Techniques
Gastrointestinal Microbiome/genetics

@article {pmid39589660,
year = {2024},
author = {Xue, X and Zhao, Z and Zhao, LB and Gao, YH and Xu, WH and Cai, WM and Chen, SH and Li, TJ and Nie, TY and Rui, D and Ma, Y and Qian, XS and Lin, JL and Liu, L},
title = {Gut microbiota changes in healthy individuals, obstructive sleep apnea patients, and patients treated using continuous positive airway pressure: a whole-genome metagenomic analysis.},
journal = {Sleep & breathing = Schlaf & Atmung},
volume = {29},
number = {1},
pages = {11},
pmid = {39589660},
issn = {1522-1709},
support = {22BJZ52//Military Health Care Project/ ; 23BJZ27//Military Health Care Project/ ; SYDW_KY[2021]04//Military experimental animal special research project/ ; },
mesh = {Humans ; *Continuous Positive Airway Pressure ; *Sleep Apnea, Obstructive/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Middle Aged ; Female ; Adult ; *Metagenomics ; Polysomnography ; },
abstract = {PURPOSE: This study investigated variations in gut microbiota among severe obstructive sleep apnea (OSA) patients and changes in gut microbiota after continuous positive airway pressure (CPAP) treatment.

METHOD: From November 2020 to August 2021, laboratory-based polysomnography (PSG) was used to measure sleep parameters in healthy controls, severe OSA patients, and severe OSA patients treated with CPAP for three months. A fully automated biochemical analyzer was used to evaluate routine blood tests and biochemical indicators. Whole-genome metagenomic analysis was used to determine the microbial composition of gut samples from all participants. The relationships between gut microbiota and hypertension were examined using correlation analysis.

RESULT: The relative abundances of Bacteroides, Firmicutes, and Parabacteroides were significantly lower at the species level. Enterobacterales and Turicibacter were significantly higher in participants with severe OSA than healthy controls. Negative correlations were identified between Bacteroides coprocola and systolic blood pressure (SBP) (r =  - 0.710, P = 0.003) and diastolic blood pressure (DBP) (r =  - 0.615, P = 0.015). Conversely, a positive correlation was found between Escherichia coli and SBP (r = 0.568, P = 0.027).

CONCLUSION: The metabolic pathways and gut microbiota differed significantly between the control group and individuals with severe OSA. Additionally, CPAP therapy substantially changed the metabolic pathways and gut microbial composition among patients diagnosed with severe OSA. Correlation analysis further revealed a strong association between Escherichia coli, Bacteroides coprocola, and blood pressure levels.},
}

Humans
*Continuous Positive Airway Pressure
*Sleep Apnea, Obstructive/therapy/microbiology
*Gastrointestinal Microbiome/physiology/genetics
Male
Middle Aged
Female
Adult
*Metagenomics
Polysomnography

@article {pmid39589588,
year = {2024},
author = {Wanna, W and Aucharean, C and Jaeram, N},
title = {Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {10},
pmid = {39589588},
issn = {1436-2236},
support = {SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; PSU_PHD2565-004//The Graduate School, Prince of Songkla University/ ; },
mesh = {Animals ; *Penaeidae/microbiology/virology ; *White spot syndrome virus 1/genetics ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Disease Resistance/genetics ; Metagenome ; },
abstract = {Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.},
}

Animals
*Penaeidae/microbiology/virology
*White spot syndrome virus 1/genetics
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Disease Resistance/genetics
Metagenome

@article {pmid39588334,
year = {2024},
author = {Zhang, J and Wu, L and Zhang, Z and Li, D and Han, R and Ye, L and Zhang, Y and Hong, J and Gu, W},
title = {Gut microbiota and metabolic profiles in adults with unclassified diabetes: a cross-sectional study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1440984},
pmid = {39588334},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Adult ; Case-Control Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Metabolome ; Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Biomarkers/blood ; Young Adult ; },
abstract = {AIMS: Our study, employing a multi-omics approach, aimed to delineate the distinct gut microbiota and metabolic characteristics in individuals under 30 with unclassified diabetes, thus shedding light on the underlying pathophysiological mechanisms.

METHODS: This age- and sex-matched case-control study involved 18 patients with unclassified diabetes, 18 patients with classic type 1 diabetes, 13 patients with type 2 diabetes, and 18 healthy individuals. Metagenomics facilitated the profiling of the gut microbiota, while untargeted liquid chromatography-mass spectrometry was used to quantify the serum lipids and metabolites.

RESULTS: Our findings revealed a unique gut microbiota composition in unclassified diabetes patients, marked by a depletion of Butyrivibrio proteoclasticus and Clostridium and an increase in Ruminococcus torques and Lachnospiraceae bacterium 8_1_57FAA. Comparative analysis identified the combined marker panel of five bacterial species, seven serum biomarkers, and three clinical parameters could differentiate patients with UDM from HCs with an AUC of 0.94 (95% CI 0.85-1). Notably, the gut microbiota structure of patients with unclassified diabetes resembled that of type 2 diabetes patients, especially regarding disrupted lipid and branched-chain amino acid metabolism.

CONCLUSIONS: Despite sharing certain metabolic features with type 2 diabetes, unclassified diabetes presents unique features. The distinct microbiota and metabolites in unclassified diabetes patients suggest a significant role in modulating glucose, lipid, and amino acid metabolism, potentially influencing disease progression. Further longitudinal studies are essential to explore therapeutic strategies targeting the gut microbiota and metabolites to modify the disease trajectory.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Male
Adult
Case-Control Studies
Cross-Sectional Studies
*Diabetes Mellitus, Type 2/microbiology/metabolism/blood
*Metabolome
Diabetes Mellitus, Type 1/microbiology/metabolism/blood
Biomarkers/blood
Young Adult

@article {pmid39587811,
year = {2024},
author = {Xu, N and Chen, B and Wang, Y and Lei, C and Zhang, Z and Ye, Y and Jin, M and Zhang, Q and Lu, T and Dong, H and Shou, J and Penuelas, J and Zhu, YG and Qian, H},
title = {Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Microbial Index for Sustainable Agriculture at Global Scale.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17596},
doi = {10.1111/gcb.17596},
pmid = {39587811},
issn = {1365-2486},
support = {22376187//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 21976161//National Natural Science Foundation of China/ ; LZ23B070001//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; MMLKF23-03//Open Funding Project of the State Key Laboratory of Microbial Metabolism/ ; TED2021-132627 B-I00//MCIN, AEI/10.13039/501100011033 European Union Next Generation EU/PRTR/ ; PID2022-140808NB-I00//Spanish Government grants/ ; },
mesh = {*Soil Microbiology ; *Agriculture/methods ; *Pesticides/analysis ; Microbiota ; Sustainable Development ; Soil/chemistry ; Metagenome ; Soil Pollutants/analysis ; Machine Learning ; },
abstract = {Soil microbiota in intensive agriculture are threatened by pesticides, economic activities, and land-use changes. However, the interactions among these anthropogenic factors remain underexplored. By analyzing 2356 soil metagenomes from around the world, we developed a comprehensive soil health-microbial index that integrates microbial diversity, nutrient cycling potential, metabolic potential, primary productivity, and health risks to assess how the soil microbiota respond to anthropogenic factors. Our results indicated that the health-microbial index was the lowest with severe pesticide contamination. Pesticides, in combination with other anthropogenic and climatic factors, exacerbate the decline in this index. Machine learning predictions suggest that the health-microbial index in approximately 26% of global farmland could decline between 2015 and 2040, even under sustainable development scenarios. Even with strategies to reduce pesticide usage, we cannot completely halt the decline in the health-microbial index. Our findings highlight that sustaining soil microbial health on a global scale requires addressing not only pesticide management but also broader anthropogenic impacts.},
}

*Soil Microbiology
*Agriculture/methods
*Pesticides/analysis
Microbiota
Sustainable Development
Soil/chemistry
Metagenome
Soil Pollutants/analysis
Machine Learning

@article {pmid39587335,
year = {2024},
author = {Liu, Y and Du, S and Sun, L and Li, Y and Liu, M and Sun, P and Bai, B and Ge, G and Jia, Y and Wang, Z},
title = {Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1565},
pmid = {39587335},
issn = {2399-3642},
mesh = {*Volatile Organic Compounds/metabolism/analysis ; *Silage/microbiology/analysis ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; *Medicago sativa/microbiology/metabolism ; Lactobacillales/metabolism/genetics ; Lactobacillus plantarum/metabolism/genetics ; },
abstract = {Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and screened Pediococcus pentosaceus (PP) on quality, microbial community, and VOCs of alfalfa silage based on volatile metabolomics and metagenomics. The results showed that the LP and PP groups had higher sensory and quality grades, and the dominant bacteria were Lactiplantibacillus plantarum and Pediococcus pentosaceus. The main VOCs in alfalfa silage were terpenoids (25.29%), esters (17.08%), and heterocyclic compounds (14.43%), and esters such as methyl benzoate, ethyl benzoate, and ethyl salicylate were significantly increased in the LP and PP groups (P < 0.05). Correlation analysis showed that terpenoids, esters, and alcohols with aromatic odors were positively correlated with Lactiplantibacillus plantarum and Pediococcus pentosaceus. Microbial functions in carbohydrate and amino acid metabolism, biosynthesis of secondary metabolites, and degradation of aromatic compounds were significantly enriched. In conclusion, the addition of lactic acid bacteria can increase the aromatic substances in silage and further improve silage odor and quality.},
}

*Volatile Organic Compounds/metabolism/analysis
*Silage/microbiology/analysis
*Metabolomics/methods
*Microbiota
*Metagenomics/methods
*Medicago sativa/microbiology/metabolism
Lactobacillales/metabolism/genetics
Lactobacillus plantarum/metabolism/genetics

@article {pmid39536991,
year = {2025},
author = {Li, Z and Gao, W and Yuan, H and Pan, X and Yuan, R and Wang, W and Guan, L and Hu, L and Chen, Y and Cheng, Z and He, R and Zhang, L and Yang, B and Zhu, Q and Liang, M and Seki, E and Lin, R and Chu, H and Yang, L},
title = {Suppression of intestinal Ticam1 ameliorated MASH via Akkermansia muciniphila QAA37749.1 mediated betaine transformation.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1871},
number = {1},
pages = {167571},
doi = {10.1016/j.bbadis.2024.167571},
pmid = {39536991},
issn = {1879-260X},
mesh = {Animals ; Mice ; *Akkermansia ; *Gastrointestinal Microbiome ; *Mice, Knockout ; Intestinal Mucosa/metabolism/microbiology/immunology/pathology ; Diet, High-Fat/adverse effects ; Male ; Fatty Liver/metabolism/pathology ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND & AIMS: Gut inflammation caused by diets could damage the intestinal barrier, which increases the liver exposition to pathogenic substances. Toll-IL-1 receptor (TIR) domain-containing adaptor molecule-1 (Ticam1) is a key molecule in the Toll-like receptors (TLRs) pathway, which is important for the immune defense against pathogens such as bacteria or viruses. In this study, mouse intestinal epithelial cell (IEC) Ticam1 was knocked out to suppress the intestinal inflammation response in metabolic dysfunction-associated steatohepatitis (MASH) to investigate its influence on the development of MASH.

METHODS: The IEC-specific Ticam1 knockout (Ticam1[ΔIEC]) mice and the control (Ticam1[fl/fl]) mice were fed with high-fat high-fructose diet (HFD) for 22 weeks to evaluate the gut alteration and the MASH-associated disorders. The intestinal secreted immunoglobulin A (sIgA) and IgA-secreting immune cells were detected. Shotgun metagenomic sequencing was used to find the gut microbiome shift in different groups. Liquid chromatography mass spectrometry was also performed to evaluate the change of serum metabolites caused by the gut microbiome alteration.

RESULTS: The gut inflammation and gut barrier dysfunction were both alleviated in HFD-fed Ticam1[ΔIEC] mice, which had improved MASH disorders compared with Ticam1[fl/fl]. Additionally, HFD-fed Ticam1[ΔIEC] mice had increased sIgA and intestinal IgA-secreting immune cells. It showed a significantly higher content of Akkermansia muciniphila. We proved that Akkermansia muciniphila encoded a protein named QAA37749.1 that could promote the conversion of choline to betaine, through which the development of MASH was inhibited in HFD-Ticam1[ΔIEC] mice.

CONCLUSION: Deletion of IEC Ticam1 alleviated MASH disorder and gut dysfunction in mice. It enhanced the level of intestinal sIgA and the growth of Akkermansia muciniphila, which supported the betaine transformation by QAA37749.1. Suppressing IEC Ticam1 might be a promising strategy for MASH disorder.},
}

Animals
Mice
*Akkermansia
*Gastrointestinal Microbiome
*Mice, Knockout
Intestinal Mucosa/metabolism/microbiology/immunology/pathology
Diet, High-Fat/adverse effects
Male
Fatty Liver/metabolism/pathology
Mice, Inbred C57BL

@article {pmid39490442,
year = {2024},
author = {Gregoris, K and Pope, WH},
title = {Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea.},
journal = {Journal of microbiological methods},
volume = {227},
number = {},
pages = {107065},
doi = {10.1016/j.mimet.2024.107065},
pmid = {39490442},
issn = {1872-8359},
mesh = {*Lichens ; *Metagenomics/methods ; DNA, Fungal/genetics/isolation & purification ; Polymerase Chain Reaction/methods ; Microbiota/genetics ; Metagenome ; Ascomycota/genetics/classification/isolation & purification/chemistry ; },
abstract = {Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.},
}

*Lichens
*Metagenomics/methods
DNA, Fungal/genetics/isolation & purification
Polymerase Chain Reaction/methods
Microbiota/genetics
Metagenome
Ascomycota/genetics/classification/isolation & purification/chemistry

@article {pmid39482414,
year = {2024},
author = {Virachabadoss, VRA and Appavoo, MS and Paramasivam, KS and Karthikeyan, SV and Govindan, D},
title = {The addition of humic acid into soil contaminated with microplastics enhanced the growth of black gram (Vigna mungo L. Hepper) and modified the rhizosphere microbial community.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {54},
pages = {63343-63359},
pmid = {39482414},
issn = {1614-7499},
mesh = {*Humic Substances ; *Rhizosphere ; *Soil Pollutants ; *Soil Microbiology ; *Vigna/drug effects/growth & development ; *Microplastics ; *Soil/chemistry ; Microbiota/drug effects ; },
abstract = {Microplastics have polluted agricultural soils, posing a substantial risk to crop productivity. Moreover, the presence of microplastic pollution has caused a disturbance in the composition of the microbial community in the soil surrounding plant roots, therefore impacting the growth of beneficial bacteria. A study was conducted to examine if humic acid (HA) can counteract the harmful effects of microplastics (MPs) on the growth of black gram crops and the composition of the rhizosphere soil microbial community, to reduce the negative impacts of microplastics on these microorganisms and crops. The research was carried out using mud pots and the plastic utilized for the experiment consisted of 60% high-density polyethylene (HDPE) and 40% polypropylene (PP). The soil was enriched with lignite-based potassium humate, which had a pH range of 8.0-9.5 and with 65% humic acid. The experiment consisted of six treatments: T1, which served as the control without HA and MP; T2, which involved the use of HA at a concentration of 0.15% w/w; T3, which involved the use of MP at a concentration of 0.2% w/w; T4, which involved the use of MP at a concentration of 0.4% w/w; T5, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.2% w/w; and T6, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.4% w/w. The plant growth characteristics, including germination percentage, nodule number, and chlorophyll content, were measured. In addition, the DNA obtained from the rhizosphere soil was analyzed using metagenomics techniques to investigate the organization of the microbial population. Seedlings in soil polluted with MP exhibited delayed germination compared to seedlings in uncontaminated soil. Following 60 days of growth, the soil samples treated with T5 (0.2% MP and 0.15% HA w/w) had the highest population of bacteria and rhizobium, with counts 5.58 ± 0.02 and 4.90 ± 0.02 CFU g[-1] soil. The plants cultivated in T5 had the most elevated chlorophyll-a concentration (1.340 ± 0.06 mg g[-1]), and chlorophyll-b concentration (0.62 ± 0.02 mg g[-1]) while those cultivated in T3 displayed the lowest concentration of chlorophyll-a (0.59 ± 0.02 mg g[-1]) and chlorophyll-b (0.21 ± 0.04 mg g[-1]). Within the phylum, Proteobacteria had the highest prevalence in all treatments. However, when the soil was polluted with MPs, its relative abundance was reduced by 8.4% compared to the control treatment (T1). Conversely, treatment T5 had a 3.76% rise in relative abundance when compared to treatment T3. The predominant taxa found in soil polluted with MP were Sphingomonas and Bacillus, accounting for 19.3% of the total. Sphingomonas was the predominant genus (21.2%) in soil polluted with MP and supplemented with humic acid. Humic acid can be used as a soil amendment to mitigate the negative effects of MPs and enhance their positive advantages. Research has demonstrated that incorporating humic acid into soil is a viable method for maintaining the long-term integrity of soil's physical, chemical, and biological characteristics.},
}

*Humic Substances
*Rhizosphere
*Soil Pollutants
*Soil Microbiology
*Vigna/drug effects/growth & development
*Microplastics
*Soil/chemistry
Microbiota/drug effects

@article {pmid39587088,
year = {2024},
author = {Honorato, L and Paião, HGO and da Costa, AC and Tozetto-Mendoza, TR and Mendes-Correa, MC and Witkin, SS},
title = {Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {137},
pmid = {39587088},
issn = {2055-5008},
mesh = {Female ; Humans ; *Metagenomics/methods ; *Viruses/genetics/classification ; *Virome ; Microbiota ; Genitalia, Female/virology/microbiology ; Metagenome ; },
abstract = {The lower female reproductive tract (FRT) hosts a complex microbial environment, including eukaryotic and prokaryotic viruses (the virome), whose roles in health and disease are not fully understood. This review consolidates findings on FRT virome composition, revealing the presence of various viral families and noting significant gaps in knowledge. Understanding interactions between the virome, microbiome, and immune system will provide novel insights for preventing and managing lower genital tract disorders.},
}

Female
Humans
*Metagenomics/methods
*Viruses/genetics/classification
*Virome
Microbiota
Genitalia, Female/virology/microbiology
Metagenome

@article {pmid39586993,
year = {2024},
author = {Zhao, Y and Bhatnagar, S},
title = {Epigenetic Modulations by Microbiome in Breast Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1465},
number = {},
pages = {55-69},
doi = {10.1007/978-3-031-66686-5_4},
pmid = {39586993},
issn = {0065-2598},
mesh = {Humans ; *Breast Neoplasms/genetics/microbiology ; *Epigenesis, Genetic ; Female ; *Tumor Microenvironment/genetics ; *Gene Expression Regulation, Neoplastic ; Microbiota/genetics ; Animals ; DNA Methylation ; Gastrointestinal Microbiome/genetics ; },
abstract = {Recent studies have identified a critical role of the diverse and dynamic microbiome in modulating various aspects of host physiology and intrinsic processes. However, the altered microbiome has also become a hallmark of cancer, which could influence the tumor microenvironment. Aberrations in epigenetic regulation of tumor suppressors, apoptotic genes, and oncogenes can accentuate breast cancer onset and progression. Interestingly, recent studies have established that the microbiota modulates the epigenetic mechanisms at global and gene-specific levels. While the mechanistic basis is unclear, the cross-talk between the microbiome and epigenetics influences breast cancer trajectory. Here, we review different epigenetic mechanisms of mammalian gene expression and summarize the host-associated microbiota distributed across the human body and their influence on cancer and other disease-related genes. Understanding this complex relationship between epigenetics and the microbiome holds promise for new insights into effective therapeutic strategies for breast cancer patients.},
}

Humans
*Breast Neoplasms/genetics/microbiology
*Epigenesis, Genetic
Female
*Tumor Microenvironment/genetics
*Gene Expression Regulation, Neoplastic
Microbiota/genetics
Animals
DNA Methylation
Gastrointestinal Microbiome/genetics

@article {pmid39585984,
year = {2024},
author = {Padhi, C and Field, CM and Forneris, CC and Olszewski, D and Fraley, AE and Sandu, I and Scott, TA and Farnung, J and Ruscheweyh, HJ and Narayan Panda, A and Oxenius, A and Greber, UF and Bode, JW and Sunagawa, S and Raina, V and Suar, M and Piel, J},
title = {Metagenomic study of lake microbial mats reveals protease-inhibiting antiviral peptides from a core microbiome member.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {49},
pages = {e2409026121},
doi = {10.1073/pnas.2409026121},
pmid = {39585984},
issn = {1091-6490},
support = {1-001369-000//Promedica Stiftung/ ; 205320_185077//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205320_219638//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 310030_212802//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; n/a//Peter und Traudl Engelhorn Stiftung (Peter and Traudl Engelhorn Foundation)/ ; 897571//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
mesh = {*Lakes/microbiology ; *Antiviral Agents/pharmacology/chemistry ; *Microbiota ; *Metagenomics/methods ; Protease Inhibitors/pharmacology/metabolism ; Peptides/metabolism/chemistry ; Multigene Family ; Metagenome ; India ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {In contrast to the large body of work on bioactive natural products from individually cultivated bacteria, the chemistry of environmental microbial communities remains largely elusive. Here, we present a comprehensive bioinformatic and functional study on a complex and interaction-rich ecosystem, algal-bacterial (microbial) mats of Lake Chilika in India, Asia's largest brackish water body. We report the bacterial compositional dynamics over the mat life cycle, >1,300 reconstructed environmental genomes harboring >2,200 biosynthetic gene clusters (BGCs), the successful cultivation of a widespread core microbiome member belonging to the genus Rheinheimera, heterologous reconstitution of two silent Rheinheimera biosynthetic pathways, and new compounds with potent protease inhibitory and antiviral activities. The identified substances, posttranslationally modified peptides from the graspetide and spliceotide families, were targeted among the large BGC diversity by applying a strategy focusing on recurring multi-BGC loci identified in diverse samples, suggesting their presence in successful colonizers. In addition to providing broad insights into the biosynthetic potential of a poorly studied community from sampling to bioactive substances, the study highlights the potential of ribosomally synthesized and posttranslationally modified peptides as a large, underexplored resource for antiviral drug discovery.},
}

*Lakes/microbiology
*Antiviral Agents/pharmacology/chemistry
*Microbiota
*Metagenomics/methods
Protease Inhibitors/pharmacology/metabolism
Peptides/metabolism/chemistry
Multigene Family
Metagenome
India
Bacteria/drug effects/genetics/metabolism

@article {pmid39546167,
year = {2024},
author = {Rajeev, M and Cho, JC},
title = {Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {62},
number = {11},
pages = {985-997},
pmid = {39546167},
issn = {1976-3794},
mesh = {*Aquaculture ; *RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae/genetics/classification/isolation & purification/metabolism ; Animals ; Republic of Korea ; China ; Metagenomics ; Vietnam ; Phylogeny ; Microbiota ; Metagenome ; Seawater/microbiology ; },
abstract = {Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.},
}

*Aquaculture
*RNA, Ribosomal, 16S/genetics
*Rhodobacteraceae/genetics/classification/isolation & purification/metabolism
Animals
Republic of Korea
China
Metagenomics
Vietnam
Phylogeny
Microbiota
Metagenome
Seawater/microbiology

@article {pmid39526896,
year = {2024},
author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L},
title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.},
journal = {Food & function},
volume = {15},
number = {23},
pages = {11667-11685},
doi = {10.1039/d4fo02704c},
pmid = {39526896},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Diet, High-Fat/adverse effects
*Cognitive Dysfunction
*Mice, Inbred C57BL
*Chenopodium quinoa/chemistry
Male
*Hordeum/chemistry
*Fermentation
Neuroinflammatory Diseases/metabolism
Lactobacillus
Hippocampus/metabolism
Brain-Gut Axis
Bacteria/classification/genetics/isolation & purification

@article {pmid39189041,
year = {2024},
author = {Haussmann, AJ and McMahan, ZH and Volkmann, ER},
title = {Understanding the gastrointestinal microbiome in systemic sclerosis: methodological advancements and emerging research.},
journal = {Current opinion in rheumatology},
volume = {36},
number = {6},
pages = {401-409},
doi = {10.1097/BOR.0000000000001048},
pmid = {39189041},
issn = {1531-6963},
mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Fecal Microbiota Transplantation/methods ; },
abstract = {PURPOSE OF REVIEW: This review highlights the role of the gastrointestinal (GI) microbiome in systemic sclerosis (SSc). We describe techniques for evaluating the GI microbiome in humans, and emerging research linking GI microbiome alterations (i.e., dysbiosis) and distinct SSc clinical manifestations. We also address the evolving treatment landscape targeting dysbiosis in SSc.

RECENT FINDINGS: Recent literature brings into focus the complex relationship between the GI microbiome and SSc pathogenesis. Advanced techniques (e.g., shotgun metagenomics, meta-transcriptomics) provide deeper insights into microbial taxonomy and active gene expression, exposing dysbiosis as a potential driver of SSc. New studies demonstrate that SSc patients who possess specific SSc clinical features, (e.g., interstitial lung disease), have unique GI microbiome profiles.

SUMMARY: Dysbiosis is associated with specific clinical features in patients with SSc. New tools for studying the GI microbiome have furthered our understanding of the relationship between dysbiosis and SSc complications. Therapeutic avenues such as dietary adjustments, probiotics, antibiotics, mindfulness practices, and fecal transplants offer potential for managing SSc and preventing its progression through GI microbiome modulation. By clarifying what is known about the relationship between the GI dysbiosis, GI dysfunction, and SSc, this review enhances our understanding of SSc pathogenesis and proposes targeted interventions.},
}

Humans
*Scleroderma, Systemic/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Fecal Microbiota Transplantation/methods

@article {pmid39582065,
year = {2024},
author = {Velsko, IM and Fagernäs, Z and Tromp, M and Bedford, S and Buckley, HR and Clark, G and Dudgeon, J and Flexner, J and Galipaud, JC and Kinaston, R and Lewis, CM and Matisoo-Smith, E and Nägele, K and Ozga, AT and Posth, C and Rohrlach, AB and Shing, R and Simanjuntak, T and Spriggs, M and Tamarii, A and Valentin, F and Willie, E and Warinner, C},
title = {Exploring the potential of dental calculus to shed light on past human migrations in Oceania.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10191},
pmid = {39582065},
issn = {2041-1723},
support = {EXC 2051, 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SRC 8038-06//National Geographic Society/ ; },
mesh = {Humans ; *Human Migration/history ; *Dental Calculus/microbiology/history ; Oceania ; *Microbiota/genetics ; Archaeology ; Phylogeny ; Pacific Islands ; Asia, Southeastern ; Metagenomics/methods ; DNA, Ancient/analysis ; History, Ancient ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.},
}

Humans
*Human Migration/history
*Dental Calculus/microbiology/history
Oceania
*Microbiota/genetics
Archaeology
Phylogeny
Pacific Islands
Asia, Southeastern
Metagenomics/methods
DNA, Ancient/analysis
History, Ancient
Bacteria/genetics/classification/isolation & purification