@article {pmid39242535,
year = {2024},
author = {Attrah, M and Schärer, MR and Esposito, M and Gionchetta, G and Bürgmann, H and Lens, PNL and Fenner, K and van de Vossenberg, J and Robinson, SL},
title = {Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {164},
pmid = {39242535},
issn = {2049-2618},
support = {109070/WT_/Wellcome Trust/United Kingdom ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 200021L_201006//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Biofilms/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Rivers/microbiology ; *Metagenomics ; Microbiota/drug effects ; Bacteria/genetics/classification/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Planctomycetales/genetics/drug effects ; Metagenome ; Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.

RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.

CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.},
}

*Biofilms/drug effects
*Wastewater/microbiology
*beta-Lactamases/genetics
*Rivers/microbiology
*Metagenomics
Microbiota/drug effects
Bacteria/genetics/classification/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
Planctomycetales/genetics/drug effects
Metagenome
Bacterial Proteins/genetics/metabolism

@article {pmid39239875,
year = {2024},
author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L},
title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2399260},
doi = {10.1080/19490976.2024.2399260},
pmid = {39239875},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; },
abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.},
}

Animals
*Gastrointestinal Microbiome
Humans
*Liver Cirrhosis/microbiology/metabolism
Mice
*Amino Acids/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
Male
*Liver/metabolism/pathology/microbiology
Female
Feces/microbiology
Mice, Inbred C57BL
Middle Aged
Fatty Liver/metabolism/microbiology
Disease Models, Animal
Metagenome
Adult

@article {pmid39137550,
year = {2024},
author = {Gao, SM and Wang, P and Li, Q and Shu, WS and Tang, LY and Lin, ZL and Li, JT and Huang, LN},
title = {Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135478},
doi = {10.1016/j.jhazmat.2024.135478},
pmid = {39137550},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; *Mining ; *Microbiota ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; China ; Metagenomics ; Acids/metabolism ; Microbial Interactions ; },
abstract = {The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.},
}

*Geologic Sediments/microbiology
*Mining
*Microbiota
*Biodegradation, Environmental
Bacteria/metabolism/genetics
China
Metagenomics
Acids/metabolism
Microbial Interactions

@article {pmid39089643,
year = {2024},
author = {Gautam, J and Aggarwal, H and Kumari, D and Gupta, SK and Kumar, Y and Dikshit, M},
title = {A methionine-choline-deficient diet induces nonalcoholic steatohepatitis and alters the lipidome, metabolome, and gut microbiome profile in the C57BL/6J mouse.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1869},
number = {8},
pages = {159545},
doi = {10.1016/j.bbalip.2024.159545},
pmid = {39089643},
issn = {1879-2618},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/microbiology/etiology/pathology ; *Methionine/deficiency/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; Male ; *Metabolome ; Lipidomics ; Choline Deficiency/metabolism ; Liver/metabolism/pathology ; Choline/metabolism ; Lipid Metabolism ; Disease Models, Animal ; Diet/adverse effects ; },
abstract = {The methionine-choline-deficient (MCD) diet-induced non-alcoholic steatohepatitis (NASH) in mice is a well-established model. Our study aims to elucidate the factors influencing liver pathology in the MCD mouse model by examining physiological, biochemical, and molecular changes using histology, molecular techniques, and OMICS approaches (lipidomics, metabolomics, and metagenomics). Male C57BL/6J mice were fed a standard chow diet, a methionine-choline-sufficient (MCS) diet, or an MCD diet for 10 weeks. The MCD diet resulted in reduced body weight and fat mass, along with decreased plasma triglyceride, cholesterol, glucose, and insulin levels. However, it notably induced steatosis, inflammation, and alterations in gene expression associated with lipogenesis, inflammation, fibrosis, and the synthesis of apolipoproteins, sphingolipids, ceramides, and carboxylesterases. Lipid analysis revealed significant changes in plasma and tissues: most ceramide non-hydroxy-sphingosine lipids significantly decreased in the liver and plasma but increased in the adipose tissue of MCD diet-fed animals. Oxidized glycerophospholipids mostly increased in the liver but decreased in the adipose tissue of the MCD diet-fed group. The gut microbiome of the MCD diet-fed group showed an increase in Firmicutes and a decrease in Bacteroidetes and Actinobacteria. Metabolomic profiling demonstrated that the MCD diet significantly altered amino acid biosynthesis, metabolism, and nucleic acid metabolism pathways in plasma, liver, fecal, and cecal samples. LC-MS data indicated higher total plasma bile acid intensity and reduced fecal glycohyodeoxycholic acid intensity in the MCD diet group. This study demonstrates that although the MCD diet induces hepatic steatosis, the mechanisms underlying NASH in this model differ from those in human NASH pathology.},
}

Animals
*Non-alcoholic Fatty Liver Disease/metabolism/microbiology/etiology/pathology
*Methionine/deficiency/metabolism
*Gastrointestinal Microbiome
Mice
*Mice, Inbred C57BL
Male
*Metabolome
Lipidomics
Choline Deficiency/metabolism
Liver/metabolism/pathology
Choline/metabolism
Lipid Metabolism
Disease Models, Animal
Diet/adverse effects

@article {pmid39032544,
year = {2024},
author = {Ioannou, M and Borkent, J and Andreu-Sánchez, S and Wu, J and Fu, J and Sommer, IEC and Haarman, BCM},
title = {Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study.},
journal = {Brain, behavior, and immunity},
volume = {121},
number = {},
pages = {165-175},
doi = {10.1016/j.bbi.2024.07.009},
pmid = {39032544},
issn = {1090-2139},
mesh = {Humans ; *Schizophrenia/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Bipolar Disorder/microbiology ; Adult ; Middle Aged ; *Metagenome ; Metagenomics/methods ; Antipsychotic Agents/therapeutic use/pharmacology ; Bacteria/genetics ; },
abstract = {BACKGROUND: Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.

METHODS: In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol.

RESULTS: The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.

CONCLUSIONS: Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.},
}

Humans
*Schizophrenia/microbiology
*Gastrointestinal Microbiome/genetics
Female
Male
*Bipolar Disorder/microbiology
Adult
Middle Aged
*Metagenome
Metagenomics/methods
Antipsychotic Agents/therapeutic use/pharmacology
Bacteria/genetics

@article {pmid39019160,
year = {2024},
author = {Zhu, Y and Yeo, EN and Smith, KM and Greenberg, AS and Rowan, S},
title = {Aging Modulates the Effect of Dietary Glycemic Index on Gut Microbiota Composition in Mice.},
journal = {The Journal of nutrition},
volume = {154},
number = {9},
pages = {2852-2861},
doi = {10.1016/j.tjnut.2024.07.014},
pmid = {39019160},
issn = {1541-6100},
mesh = {Animals ; Male ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; *Aging ; *Glycemic Index ; Mice ; *Diet ; *Feces/microbiology/chemistry ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Gut microbiome composition profoundly impacts host physiology and is modulated by several environmental factors, most prominently diet. The composition of gut microbiota changes over the lifespan, particularly during the earliest and latest stages. However, we know less about diet-aging interactions on the gut microbiome. We previously showed that diets with different glycemic indices, based on the ratio of rapidly digested amylopectin to slowly digested amylose, led to altered composition of gut microbiota in male C57BL/6J mice.

OBJECTIVES: Here, we examined the role of aging in influencing dietary effects on gut microbiota composition and aimed to identify gut bacterial taxa that respond to diet and aging.

METHODS: We studied 3 age groups of male C57BL/6J wild-type mice: young (4 mo), middle-aged (13.5 mo), and old (22 mo), all fed either high glycemic (HG) or low glycemic (LG) diets matched for caloric content and macronutrient composition. Fecal microbiome composition was determined by 16S rDNA metagenomic sequencing and was evaluated for changes in α- and β-diversity and bacterial taxa that change by age, diet, or both.

RESULTS: Young mice displayed lower α-diversity scores than middle-aged counterparts but exhibited more pronounced differences in β-diversity between diets. In contrast, old mice had slightly lower α-diversity scores than middle-aged mice, with significantly higher β-diversity distances. Within-group variance was lowest in young, LG-fed mice and highest in old, HG-fed mice. Differential abundance analysis revealed taxa associated with both aging and diet. Most differential taxa demonstrated significant interactions between diet and aging. Notably, several members of the Lachnospiraceae family increased with aging and HG diet, whereas taxa from the Bacteroides_H genus increased with the LG diet. Akkermansia muciniphila decreased with aging.

CONCLUSIONS: These findings illustrate the complex interplay between diet and aging in shaping the gut microbiota, potentially contributing to age-related disease.},
}

Animals
Male
*Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
*Aging
*Glycemic Index
Mice
*Diet
*Feces/microbiology/chemistry
Bacteria/classification/genetics
RNA, Ribosomal, 16S

@article {pmid39237540,
year = {2024},
author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N},
title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7751},
pmid = {39237540},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Singapore ; Male ; Aged, 80 and over ; Female ; *Aging ; *Metagenome ; Asian People/genetics ; Phenotype ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; },
abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.},
}

Humans
*Gastrointestinal Microbiome/genetics
Singapore
Male
Aged, 80 and over
Female
*Aging
*Metagenome
Asian People/genetics
Phenotype
Metagenomics/methods
Bacteria/genetics/classification/metabolism/isolation & purification
Bacteroides/genetics/metabolism
Cohort Studies
Feces/microbiology

@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}

*Metagenomics/methods
*Computational Biology/methods
*Food Microbiology/methods
*Bacteria/genetics
*High-Throughput Nucleotide Sequencing/methods
Metagenome
Microbiota/genetics

@article {pmid39232827,
year = {2024},
author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH},
title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {163},
pmid = {39232827},
issn = {2049-2618},
support = {2019YFA0905600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Face/microbiology ; Middle Aged ; *Skin Aging/physiology ; Female ; Adult ; Male ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Aging ; Metagenome ; Young Adult ; High-Throughput Nucleotide Sequencing ; Sebum/metabolism ; },
abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.

RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.

CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.},
}

Humans
*Microbiota
*Skin/microbiology
*Face/microbiology
Middle Aged
*Skin Aging/physiology
Female
Adult
Male
*Bacteria/classification/genetics/isolation & purification
Aged
Aging
Metagenome
Young Adult
High-Throughput Nucleotide Sequencing
Sebum/metabolism

@article {pmid39232089,
year = {2024},
author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G},
title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20545},
pmid = {39232089},
issn = {2045-2322},
mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation & purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; },
abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.},
}

Animals
*Aedes/microbiology
Spain
*Microbiota
*Wolbachia/genetics/isolation & purification/physiology
Female
*RNA, Ribosomal, 16S/genetics
Mosquito Vectors/microbiology
Ecosystem
Male

@article {pmid39230701,
year = {2024},
author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D},
title = {Metagenomic functional profiling: to sketch or not to sketch?.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_2},
pages = {ii165-ii173},
pmid = {39230701},
issn = {1367-4811},
support = {R01GM146462/GF/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; },
abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99× faster in wall-clock time, and consumes up to 40-55× less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.

This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.},
}

*Metagenomics/methods
*Software
*Algorithms
*Metagenome/genetics
Humans
Microbiota/genetics
Databases, Genetic

@article {pmid39143383,
year = {2024},
author = {Vijayan, J and Ezhuthanikkunnel, AP and Punnorkodu, SAK and Poikayil, SS and Mohan, M and Ammanamveetil, MHA},
title = {Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {39},
pages = {52132-52146},
pmid = {39143383},
issn = {1614-7499},
mesh = {*Geologic Sediments/microbiology ; *Estuaries ; India ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.},
}

*Geologic Sediments/microbiology
*Estuaries
India
Drug Resistance, Microbial/genetics
Bacteria/genetics
Phylogeny
Biodiversity

@article {pmid39069433,
year = {2024},
author = {Tomiak, J and Stensvold, CR},
title = {Accelerating the paradigm shift in Blastocystis research.},
journal = {Trends in parasitology},
volume = {40},
number = {9},
pages = {775-776},
doi = {10.1016/j.pt.2024.07.006},
pmid = {39069433},
issn = {1471-5007},
mesh = {*Blastocystis/physiology ; *Blastocystis Infections/parasitology ; Humans ; Animals ; Gastrointestinal Microbiome/physiology ; },
abstract = {Blastocystis, once targeted as a harmful intestinal parasite, is now seen as potentially beneficial. Piperni et al. link its presence to improved gut health, higher microbial diversity, and favorable cardiometabolic outcomes, which suggests that Blastocystis might indicate a healthy diet and gut, possibly serving as a symbiont rather than a pathogen.},
}

*Blastocystis/physiology
*Blastocystis Infections/parasitology
Humans
Animals
Gastrointestinal Microbiome/physiology

@article {pmid39230075,
year = {2024},
author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I},
title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393791},
doi = {10.1080/19490976.2024.2393791},
pmid = {39230075},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; },
abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Humans
Phylogeny
Diet

@article {pmid39227168,
year = {2024},
author = {Salmaso, N and Cerasino, L and Pindo, M and Boscaini, A},
title = {Taxonomic and functional metagenomic assessment of a dolichospermum bloom in a large and deep lake south of the Alps.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae117},
pmid = {39227168},
issn = {1574-6941},
abstract = {Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome (MAG) obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.},
}

@article {pmid39089018,
year = {2024},
author = {Cui, M and Wang, M and Liu, X and Sun, H and Su, Z and Zheng, Y and Shen, Y and Wang, M},
title = {Mining and characterization of novel antimicrobial peptides from the large-scale microbiome of Shanxi aged vinegar based on metagenomics, molecular dynamics simulations and mechanism validation.},
journal = {Food chemistry},
volume = {460},
number = {Pt 2},
pages = {140646},
doi = {10.1016/j.foodchem.2024.140646},
pmid = {39089018},
issn = {1873-7072},
mesh = {*Metagenomics ; *Molecular Dynamics Simulation ; *Staphylococcus aureus/drug effects ; *Acetic Acid/chemistry/pharmacology ; *Escherichia coli/drug effects/genetics/metabolism ; Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics ; Anti-Bacterial Agents/pharmacology/chemistry ; Microbiota ; Microbial Sensitivity Tests ; Humans ; Lactobacillus/chemistry/metabolism ; },
abstract = {The study aimed to mine and characterize novel antimicrobial peptides (AMPs) from the Shanxi aged vinegar microbiome. Utilizing machine learning techniques, AlphaFold2 structure prediction and molecular dynamics simulations, six novel AMPs were innovatively mined from 98,539 peptides based on metagenomic data, of which one peptide secreted by Lactobacillus (named La-AMP) was experimentally validated to have remarkable bactericidal effects against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with high stability and no hemolytic activity. Scanning electron microscopy revealed that La-AMP caused irreversible damage to cell membranes of S. aureus and E. coli, a finding further confirmed by calcein-AM/propidium iodide staining. Additionally, La-AMP induced nucleic acid leakage and reactive oxygen species accumulation in bacterial cells. It was found to bind to DNA gyrase through salt bridges, hydrogen bonds, and hydrophobic interactions, ultimately inducing apoptosis. Thus, La-AMP exhibited encouraging promise as a valuable bioactive component for the development of natural preservatives.},
}

*Metagenomics
*Molecular Dynamics Simulation
*Staphylococcus aureus/drug effects
*Acetic Acid/chemistry/pharmacology
*Escherichia coli/drug effects/genetics/metabolism
Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics
Anti-Bacterial Agents/pharmacology/chemistry
Microbiota
Microbial Sensitivity Tests
Humans
Lactobacillus/chemistry/metabolism

@article {pmid39222347,
year = {2024},
author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A},
title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001289},
pmid = {39222347},
issn = {2057-5858},
mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention & control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.},
}

Animals
*Chickens/microbiology
*Infectious bronchitis virus/immunology/genetics
*Cecum/microbiology
*Gastrointestinal Microbiome
Vaccination
Poultry Diseases/microbiology/virology/immunology
Coronavirus Infections/veterinary/prevention & control/immunology
Viral Vaccines/immunology/genetics
Receptors, G-Protein-Coupled/genetics
Metagenome
Dendritic Cells/immunology
Bacteria/classification/genetics
Metagenomics

@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {410},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.},
}

Animals
*Manure/microbiology
*Chickens
*Composting
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Bacteria/genetics/drug effects
Microbiota/drug effects
Gene Transfer, Horizontal

@article {pmid39149810,
year = {2024},
author = {Liu, J and Wang, WJ and Xu, GF and Wang, YX and Lin, Y and Zheng, X and Yao, SH and Zheng, KH},
title = {Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (>90 Years) and Elderly (65-74 Years) Adults.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {9},
pages = {461-469},
doi = {10.1089/omi.2024.0120},
pmid = {39149810},
issn = {1557-8100},
mesh = {Humans ; Aged ; *Longevity ; *Gastrointestinal Microbiome/physiology ; Aged, 80 and over ; Male ; Female ; China ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; East Asian People ; },
abstract = {The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.},
}

Humans
Aged
*Longevity
*Gastrointestinal Microbiome/physiology
Aged, 80 and over
Male
Female
China
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
East Asian People

@article {pmid39145585,
year = {2024},
author = {Liu, B and Wang, G and Wang, L and Yan, J and Zhu, K and Liu, Q and Zhao, J and Jia, B and Fang, M and Rudich, Y and Morawska, L and Chen, J},
title = {Unraveling Cross-Organ Impacts of Airborne Pollutants: A Multiomics Study on Respiratory Exposure and Gastrointestinal Health.},
journal = {Environmental science & technology},
volume = {58},
number = {35},
pages = {15511-15521},
doi = {10.1021/acs.est.4c06035},
pmid = {39145585},
issn = {1520-5851},
mesh = {Mice ; Animals ; *Air Pollutants/toxicity ; Inhalation Exposure ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects ; Multiomics ; },
abstract = {Poor air quality is increasingly linked to gastrointestinal diseases, suggesting a potential correlation with human intestine health. However, this relationship remains largely unexplored due to limited research. This study used a controlled mouse model exposed to cooking oil fumes (COFs) and metagenomics, transcriptomics, and metabolomics to elucidate interactions between intestine microbiota and host metabolism under environmental stress. Our findings reveal that short-term COF inhalation induces pulmonary inflammation within 3 days and leads to gastrointestinal disturbances, elucidating a pathway connecting respiratory exposure to intestinal dysfunction. The exposure intensity significantly correlates with changes in intestinal tissue integrity, microbial composition, and metabolic function. Extended exposure of 7 days disrupts intestine microbiota and alters tryptophan metabolism, with further changes observed after 14 days, highlighting an adaptive response. These results highlight the vulnerability of intestinal health to airborne pollutants and suggest a pathway through which inhaled pollutants may affect distant organ systems.},
}

Mice
Animals
*Air Pollutants/toxicity
Inhalation Exposure
Gastrointestinal Microbiome/drug effects
Gastrointestinal Tract/drug effects
Multiomics

@article {pmid38977906,
year = {2024},
author = {Su, Q and Wong, OWH and Lu, W and Wan, Y and Zhang, L and Xu, W and Li, MKT and Liu, C and Cheung, CP and Ching, JYL and Cheong, PK and Leung, TF and Chan, S and Leung, P and Chan, FKL and Ng, SC},
title = {Multikingdom and functional gut microbiota markers for autism spectrum disorder.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2344-2355},
pmid = {38977906},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/diagnosis ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; *Feces/microbiology ; *Biomarkers/analysis ; Infant ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics/methods ; Machine Learning ; Archaea/genetics/metabolism/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Viruses/genetics/isolation & purification/classification ; Metagenome ; },
abstract = {Associations between the gut microbiome and autism spectrum disorder (ASD) have been investigated although most studies have focused on the bacterial component of the microbiome. Whether gut archaea, fungi and viruses, or function of the gut microbiome, is altered in ASD is unclear. Here we performed metagenomic sequencing on faecal samples from 1,627 children (aged 1-13 years, 24.4% female) with or without ASD, with extensive phenotype data. Integrated analyses revealed that 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes and 12 metabolic pathways were altered in children with ASD. Machine learning using single-kingdom panels showed area under the curve (AUC) of 0.68 to 0.87 in differentiating children with ASD from those that are neurotypical. A panel of 31 multikingdom and functional markers showed a superior diagnostic accuracy with an AUC of 0.91, with comparable performance for males and females. Accuracy of the model was predominantly driven by the biosynthesis pathways of ubiquinol-7 or thiamine diphosphate, which were less abundant in children with ASD. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiota markers as non-invasive diagnostic tools in ASD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/microbiology/diagnosis
Female
Male
Child
Child, Preschool
Adolescent
*Feces/microbiology
*Biomarkers/analysis
Infant
*Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics/methods
Machine Learning
Archaea/genetics/metabolism/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
Viruses/genetics/isolation & purification/classification
Metagenome

@article {pmid38141256,
year = {2024},
author = {Hassan-Zahraee, M and Ye, Z and Xi, L and Dushin, E and Lee, J and Romatowski, J and Leszczyszyn, J and Danese, S and Sandborn, WJ and Banfield, C and Gale, JD and Peeva, E and Longman, RS and Hyde, CL and Hung, KE},
title = {Baseline Serum and Stool Microbiome Biomarkers Predict Clinical Efficacy and Tissue Molecular Response After Ritlecitinib Induction Therapy in Ulcerative Colitis.},
journal = {Journal of Crohn's & colitis},
volume = {18},
number = {9},
pages = {1361-1370},
doi = {10.1093/ecco-jcc/jjad213},
pmid = {38141256},
issn = {1876-4479},
support = {//Pfizer/ ; },
mesh = {Humans ; *Colitis, Ulcerative/drug therapy/blood/microbiology ; *Feces/microbiology/chemistry ; *Biomarkers/blood/analysis ; Male ; Female ; Adult ; Middle Aged ; Gastrointestinal Microbiome/drug effects ; Proteomics/methods ; Treatment Outcome ; Remission Induction ; Induction Chemotherapy/methods ; Metagenomics/methods ; },
abstract = {BACKGROUND AND AIMS: Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well-tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis [UC]. The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.

METHODS: Tissue and peripheral blood proteomics, transcriptomics, and faecal metagenomics were performed on samples before and after 8 weeks of oral ritlecitinib induction therapy [20 mg, 70 mg, 200 mg, or placebo once daily, N = 39, 41, 33, and 18, respectively]. Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of faecal metagenomics was used to differentiate responders and nonresponders.

RESULTS: Peripheral blood serum proteomics identified four baseline serum markers [LTA, CCL21, HLA-E, MEGF10] predictive of modified clinical remission [MR], endoscopic improvement [EI], histological remission [HR], and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline [false discovery rate of <0.05]; of these, changes in four [IL4R, TNFRSF4, SPINK4, and LAIR-1] predicted concurrent EI and HR responses. Faecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.

CONCLUSIONS: Blood and microbiome biomarkers stratify endoscopic, histological, and tissue molecular responses to ritlecitinib, which may help guide future precision medicine approaches to UC treatment. ClinicalTrials.gov NCT02958865.},
}

Humans
*Colitis, Ulcerative/drug therapy/blood/microbiology
*Feces/microbiology/chemistry
*Biomarkers/blood/analysis
Male
Female
Adult
Middle Aged
Gastrointestinal Microbiome/drug effects
Proteomics/methods
Treatment Outcome
Remission Induction
Induction Chemotherapy/methods
Metagenomics/methods

@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae424},
pmid = {39222062},
issn = {1477-4054},
support = {P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
Computational Biology/methods
Metagenome
High-Throughput Nucleotide Sequencing/methods
Software
Algorithms
Sequence Analysis, DNA/methods

@article {pmid39218875,
year = {2024},
author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J},
title = {Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {346},
pmid = {39218875},
issn = {1741-7015},
mesh = {Humans ; Female ; Male ; *Transgender Persons ; Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Prospective Studies ; Metagenome ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts.

METHODS: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT.

RESULTS: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R[2] = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism.

CONCLUSIONS: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes.

TRIAL REGISTRATION: Clinicaltrials.gov NCT02185274.},
}

Humans
Female
Male
*Transgender Persons
Adult
*Feces/microbiology
*Gastrointestinal Microbiome/drug effects/genetics
Prospective Studies
Metagenome
Young Adult
Middle Aged

@article {pmid39217389,
year = {2024},
author = {Zhang, Y and Cheng, TY and Liu, GH and Liu, L and Duan, DY},
title = {Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {370},
pmid = {39217389},
issn = {1756-3305},
support = {No. 31902294//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Sheep ; Cattle ; Female ; *Metagenome ; *Ixodidae/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/isolation & purification/genetics ; Tick Infestations/veterinary/parasitology ; Sheep Diseases/microbiology/parasitology ; China ; Metagenomics ; Tibet ; Cattle Diseases/microbiology/parasitology ; },
abstract = {BACKGROUND: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.

METHODS: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.

RESULTS: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.

CONCLUSIONS: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.},
}

Animals
Sheep
Cattle
Female
*Metagenome
*Ixodidae/microbiology
Gastrointestinal Microbiome
Bacteria/classification/isolation & purification/genetics
Tick Infestations/veterinary/parasitology
Sheep Diseases/microbiology/parasitology
China
Metagenomics
Tibet
Cattle Diseases/microbiology/parasitology

@article {pmid39115410,
year = {2024},
author = {Moncada, C and Arnosti, C and Brüwer, JD and de Beer, D and Amann, R and Knittel, K},
title = {Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae159},
pmid = {39115410},
issn = {1751-7370},
support = {//Max Planck Society/ ; OCE-2022952//National Science Foundation/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/metabolism/isolation & purification/genetics ; *Microbiota ; Svalbard ; Heterotrophic Processes ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.},
}

*Geologic Sediments/microbiology
*Bacteria/classification/metabolism/isolation & purification/genetics
*Microbiota
Svalbard
Heterotrophic Processes
RNA, Ribosomal, 16S/genetics

@article {pmid39098620,
year = {2024},
author = {Padasas-Adalla, CS and Ortega-Kindica, RCMH and Lomelí-Ortega, CO and Tabugo, SRM and Balcázar, JL},
title = {A metagenomics-based approach to decipher the resistome and mobilome of two seahorse species, Hippocampus barbouri and Hippocampus comes.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {3},
pages = {107296},
doi = {10.1016/j.ijantimicag.2024.107296},
pmid = {39098620},
issn = {1872-7913},
mesh = {Animals ; *Smegmamorpha/microbiology ; *Metagenomics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Skin/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbiota/genetics/drug effects ; Interspersed Repetitive Sequences/genetics ; },
abstract = {OBJECTIVE: This study aimed to explore the abundance and diversity of antibiotic resistance genes (ARGs) in seahorses (Hippocampus barbouri and Hippocampus comes) and their surrounding environment.

METHODS: A combination of shotgun metagenomics and bioinformatics was used to investigate the resistome of both seahorse species.

RESULTS: The analyses demonstrated a higher abundance of ARGs in seahorse-associated microbiomes, particularly in skin and gut samples, compared to those from water and sediment. Interestingly, genes conferring multidrug resistance (e.g., acrB, acrF, cpxA, msbA, and oqxB) were highly prevalent in all samples, especially in skin and gut samples. High levels of genes conferring resistance to fluoroquinolones (e.g., mfd and emrB), β-lactam (e.g., blaCMY-71, blaOXA-55, and penA), aminocoumarin (e.g., mdtB and mdtC), and peptide antibiotics (arnA, pmrE, and rosA) were also observed in skin and gut samples. An enrichment of mobile genetic elements (MGEs) was also observed in the analysed samples, highlighting their potential role in facilitating the acquisition and spread of ARGs. In fact, the abundance of mobilisation (MOB) relaxases (e.g., MOBF, MOBP, MOBT, and MOBV) in gut and skin samples suggests a high potential for conjugation events.

CONCLUSIONS: The occurrence of ARGs and MGEs in seahorses and the surrounding environment raises concerns about their transmission to humans, either through direct contact or the consumption of contaminated seafood. To the best of our knowledge, this study represents the first comprehensive analysis of ARGs in seahorse-associated microbiomes, and its results emphasise the need for monitoring and controlling the spread of ARGs in environmental settings.},
}

Animals
*Smegmamorpha/microbiology
*Metagenomics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects/classification
Skin/microbiology
Drug Resistance, Multiple, Bacterial/genetics
Microbiota/genetics/drug effects
Interspersed Repetitive Sequences/genetics

@article {pmid39096506,
year = {2024},
author = {Oggerin, M and Viver, T and Brüwer, J and Voß, D and García-Llorca, M and Zielinski, O and Orellana, LH and Fuchs, BM},
title = {Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39096506},
issn = {1751-7370},
support = {//Max Planck Society/ ; SO-245//UltraPac Expedition/ ; 03G0245A//Federal Ministry of Education and Research of Germany/ ; },
mesh = {*Seawater/microbiology ; Pacific Ocean ; Alphaproteobacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; In Situ Hybridization, Fluorescence ; Ecosystem ; Phylogeny ; Microbiota ; },
abstract = {One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.},
}

*Seawater/microbiology
Pacific Ocean
Alphaproteobacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
In Situ Hybridization, Fluorescence
Ecosystem
Phylogeny
Microbiota

@article {pmid39043311,
year = {2024},
author = {Wang, X and Li, J and Wang, D and Sun, C and Zhang, X and Zhao, J and Teng, J and Wang, Q},
title = {Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124591},
doi = {10.1016/j.envpol.2024.124591},
pmid = {39043311},
issn = {1873-6424},
mesh = {*Geologic Sediments/chemistry/microbiology ; *Microplastics/toxicity ; *Nitrogen Cycle ; *Water Pollutants, Chemical/metabolism/analysis ; *Estuaries ; Metagenomics ; Nitrogen/metabolism ; Environmental Monitoring ; Microbiota/drug effects ; },
abstract = {Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.},
}

*Geologic Sediments/chemistry/microbiology
*Microplastics/toxicity
*Nitrogen Cycle
*Water Pollutants, Chemical/metabolism/analysis
*Estuaries
Metagenomics
Nitrogen/metabolism
Environmental Monitoring
Microbiota/drug effects

@article {pmid39019308,
year = {2024},
author = {Ewere, EE and White, S and Mauleon, R and Benkendorff, K},
title = {Soil microbial communities and degradation of pesticides in greenhouse effluent through a woodchip bioreactor.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124561},
doi = {10.1016/j.envpol.2024.124561},
pmid = {39019308},
issn = {1873-6424},
mesh = {*Bioreactors/microbiology ; *Soil Microbiology ; *Biodegradation, Environmental ; *Pesticides/metabolism/analysis ; Soil Pollutants/analysis/metabolism ; Microbiota ; Agriculture ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; },
abstract = {Pesticides, including insecticides and fungicides, are major contaminants in the effluent from intensive agricultural systems, such as greenhouses. Because of their constant use and persistence, some pesticides can accumulate in soil and/or run off into adjacent waterways. Microbial communities in soil can degrade some pesticides, and bioreactors with enhanced microbial communities have the potential to facilitate decontamination before the effluent is released into the environment. In this study, we sampled the soil along a gradient from immediately below greenhouses, into, through and below a bioreactor. Multi-analyte pesticide screening was undertaken along with shotgun metagenomic sequencing, to assess microbial community taxonomic profiles and metabolic pathway responses for functional analysis. Two insecticides (imidacloprid and fipronil) and nine fungicides were identified in the soil samples, with a general decrease in most pesticides with increasing distance from the greenhouses. Diversity indexes of taxonomic profiles show changes in the microbial community along the gradient. In particular, microbial communities were significantly different in the bioreactor, with lower Shannon diversity compared to immediately below the greenhouses, in the channels leading into the bioreactor and further downstream. Metabolic pathway analysis revealed significant changes in a wide range of core housekeeping genes such as protein/amino acid synthesis and lipid/fatty acid biosynthesis among the sampling sites. The result demonstrates that the composition and potential functional pathways of the microbial community shifted towards an increased tendency for phytol and contaminant degradation in the bioreactor, facilitated by high organic matter content. This highlights the potential to use enhanced microbial communities within bioreactors to reduce contamination by some pesticides in sediment receiving run-off from greenhouses.},
}

*Bioreactors/microbiology
*Soil Microbiology
*Biodegradation, Environmental
*Pesticides/metabolism/analysis
Soil Pollutants/analysis/metabolism
Microbiota
Agriculture
Bacteria/metabolism/genetics/classification
Soil/chemistry

@article {pmid39014985,
year = {2024},
author = {Duggan DiDominic, KL and Shapleigh, JP and Walter, MT and Wang, YS and Reid, MC and Regan, JM},
title = {Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix.},
journal = {Journal of environmental quality},
volume = {53},
number = {5},
pages = {565-576},
doi = {10.1002/jeq2.20600},
pmid = {39014985},
issn = {1537-2537},
support = {1922551//National Science Foundation Research Traineeship (NRT) Program/ ; 2019-67019-29461//U.S. Department of Agriculture/ ; },
mesh = {*Bioreactors ; *Wood ; *Biofilms ; *Denitrification ; Microbiota ; Nitrogen/analysis ; Bacteria/genetics/metabolism ; },
abstract = {Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.},
}

*Bioreactors
*Wood
*Biofilms
*Denitrification
Microbiota
Nitrogen/analysis
Bacteria/genetics/metabolism

@article {pmid38988320,
year = {2024},
author = {Kumar, M and Saini, HS},
title = {Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach.},
journal = {Journal of basic microbiology},
volume = {64},
number = {9},
pages = {e2400303},
doi = {10.1002/jobm.202400303},
pmid = {38988320},
issn = {1521-4028},
support = {//This study was funded by Department of Biotechnology (DBT), Ministry of Science and Technology, New Delhi (India) (Project number BT/PR7535/BCE/8/960/2013)./ ; },
mesh = {*Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Soil Microbiology ; *Metagenomics ; Wastewater/microbiology ; Phylogeny ; Biodiversity ; Proteobacteria/genetics/classification/metabolism/isolation & purification ; DNA, Bacterial/genetics ; Metals, Heavy/metabolism/analysis ; Microbiota ; },
abstract = {Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.},
}

*Biodegradation, Environmental
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
*Soil Microbiology
*Metagenomics
Wastewater/microbiology
Phylogeny
Biodiversity
Proteobacteria/genetics/classification/metabolism/isolation & purification
DNA, Bacterial/genetics
Metals, Heavy/metabolism/analysis
Microbiota

@article {pmid38936492,
year = {2024},
author = {Rodriguez-Ruiz, JP and Lin, Q and Van Heirstraeten, L and Lammens, C and Stewardson, AJ and Godycki-Cwirko, M and Coenen, S and Goossens, H and Harbarth, S and Malhotra-Kumar, S and , },
title = {Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {3},
pages = {107259},
doi = {10.1016/j.ijantimicag.2024.107259},
pmid = {38936492},
issn = {1872-7913},
mesh = {Humans ; *Ciprofloxacin/therapeutic use/pharmacology ; *Oropharynx/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome/drug effects/genetics ; *Urinary Tract Infections/microbiology/drug therapy ; Aged ; Adult ; Switzerland ; Belgium ; Poland ; Drug Resistance, Bacterial ; Feces/microbiology ; Microbiota/drug effects/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland.

METHODS: Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics.

RESULTS: At the end of therapy, patients treated with both short (≤7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, β-lactam, sulphonamide, and tetracycline resistance genes.

CONCLUSION: Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.},
}

Humans
*Ciprofloxacin/therapeutic use/pharmacology
*Oropharynx/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Female
Male
Middle Aged
*Gastrointestinal Microbiome/drug effects/genetics
*Urinary Tract Infections/microbiology/drug therapy
Aged
Adult
Switzerland
Belgium
Poland
Drug Resistance, Bacterial
Feces/microbiology
Microbiota/drug effects/genetics
Metagenomics

@article {pmid39217229,
year = {2024},
author = {Gyaltshen, Y and Ishii, Y and Charvet, S and Goetz, E and Maruyama, S and Kim, E},
title = {Molecular diversity of green-colored microbial mats from hot springs of northern Japan.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {43},
pmid = {39217229},
issn = {1433-4909},
support = {KAKENHI 17H05713//Japan Society for the Promotion of Science/ ; 19H04713//Japan Society for the Promotion of Science/ ; CAREER 1453639//Division of Integrative Organismal Systems/ ; },
mesh = {*Hot Springs/microbiology ; Japan ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.},
}

*Hot Springs/microbiology
Japan
RNA, Ribosomal, 16S/genetics
Metagenome
Microbiota
Bacteria/genetics/classification/isolation & purification
Phylogeny

@article {pmid39215001,
year = {2024},
author = {Becsei, Á and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P},
title = {Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7551},
pmid = {39215001},
issn = {2041-1723},
support = {NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Seasons ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Metagenome/genetics ; Europe ; },
abstract = {Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.},
}

*Sewage/microbiology
*Metagenomics/methods
*Seasons
Humans
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*Metagenome/genetics
Europe

@article {pmid39214983,
year = {2024},
author = {Duan, Y and Santos-Júnior, CD and Schmidt, TS and Fullam, A and de Almeida, BLS and Zhu, C and Kuhn, M and Zhao, XM and Bork, P and Coelho, LP},
title = {A catalog of small proteins from the global microbiome.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7563},
pmid = {39214983},
issn = {2041-1723},
support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Microbiota/genetics ; *Open Reading Frames/genetics ; *Bacteria/genetics/classification/metabolism ; *Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; Molecular Sequence Annotation ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.},
}

*Microbiota/genetics
*Open Reading Frames/genetics
*Bacteria/genetics/classification/metabolism
*Metagenome/genetics
*Archaea/genetics/metabolism/classification
Molecular Sequence Annotation
Bacterial Proteins/genetics/metabolism

@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}

*Phylogeny
*Giant Viruses/genetics
*Genome, Viral/genetics
Drug Resistance, Microbial/genetics
Bacteriophages/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Metagenome/genetics
Gene Transfer, Horizontal
Trimethoprim/pharmacology
Drug Resistance, Bacterial/genetics

@article {pmid39209868,
year = {2024},
author = {Gonzalez, E and Lee, MD and Tierney, BT and Lipieta, N and Flores, P and Mishra, M and Beckett, L and Finkelstein, A and Mo, A and Walton, P and Karouia, F and Barker, R and Jansen, RJ and Green, SJ and Weging, S and Kelliher, J and Singh, NK and Bezdan, D and Galazska, J and Brereton, NJB},
title = {Spaceflight alters host-gut microbiota interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {71},
pmid = {39209868},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Space Flight ; Mice ; *Bacteria/classification/genetics ; Liver/microbiology ; Host Microbial Interactions ; Metagenomics/methods ; Colon/microbiology ; Bile Acids and Salts/metabolism ; Energy Metabolism ; Male ; Humans ; Mice, Inbred C57BL ; },
abstract = {The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.},
}

*Gastrointestinal Microbiome
Animals
*Space Flight
Mice
*Bacteria/classification/genetics
Liver/microbiology
Host Microbial Interactions
Metagenomics/methods
Colon/microbiology
Bile Acids and Salts/metabolism
Energy Metabolism
Male
Humans
Mice, Inbred C57BL

@article {pmid39209855,
year = {2024},
author = {Whittle, MJ and Castillo-Fernandez, J and Amos, GCA and Watson, P},
title = {Metagenomic characterisation of canine skin reveals a core healthy skin microbiome.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20104},
pmid = {39209855},
issn = {2045-2322},
mesh = {Dogs ; Animals ; *Skin/microbiology ; *Microbiota ; *Metagenomics/methods ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.},
}

Dogs
Animals
*Skin/microbiology
*Microbiota
*Metagenomics/methods
Metagenome
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}

Animals
Swine
*Virome/genetics
*Metagenomics/methods
*Gastrointestinal Microbiome
*Viruses/genetics/classification/isolation & purification
*Genome, Viral
Data Mining
Metagenome
Phylogeny

@article {pmid39209850,
year = {2024},
author = {Colman, DR and Keller, LM and Arteaga-Pozo, E and Andrade-Barahona, E and St Clair, B and Shoemaker, A and Cox, A and Boyd, ES},
title = {Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7506},
pmid = {39209850},
issn = {2041-1723},
support = {80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {*Hot Springs/microbiology/chemistry ; *Metagenome ; *Phylogeny ; Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism ; Genome, Microbial ; Ecosystem ; Microbiota/genetics ; },
abstract = {The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.},
}

*Hot Springs/microbiology/chemistry
*Metagenome
*Phylogeny
Bacteria/genetics/classification/metabolism
Hydrogen-Ion Concentration
Archaea/genetics/classification/metabolism
Genome, Microbial
Ecosystem
Microbiota/genetics

@article {pmid39206042,
year = {2024},
author = {Zhen, J and Zhang, Y and Li, Y and Zhou, Y and Cai, Y and Huang, G and Xu, A},
title = {The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1423662},
doi = {10.3389/fcimb.2024.1423662},
pmid = {39206042},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; *Carnosine/metabolism ; Male ; *Feces/microbiology ; Glucose Intolerance/metabolism ; Inflammation/metabolism ; Hep G2 Cells ; Metagenomics ; Female ; Middle Aged ; Taurochenodeoxycholic Acid/metabolism/pharmacology ; Hyperglycemia/metabolism ; Neutrophils/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/metabolism/genetics ; },
abstract = {OBJECTIVE: This study aims to investigate the pathogenesis of hyperglycemia and its associated vasculopathy using multiomics analyses in diabetes and impaired glucose tolerance, and validate the mechanism using the cell experiments.

METHODS: In this study, we conducted a comprehensive analysis of the metagenomic sequencing data of diabetes to explore the key genera related to its occurrence. Subsequently, participants diagnosed with impaired glucose tolerance (IGT), and healthy subjects, were recruited for fecal and blood sample collection. The dysbiosis of the gut microbiota (GM) and its associated metabolites were analyzed using 16S rDNA sequencing and liquid chromatograph mass spectrometry, respectively. The regulation of gene and protein expression was evaluated through mRNA sequencing and data-independent acquisition technology, respectively. The specific mechanism by which GM dysbiosis affects hyperglycemia and its related vasculopathy was investigated using real-time qPCR, Western blotting, and enzyme-linked immunosorbent assay techniques in HepG2 cells and neutrophils.

RESULTS: Based on the published data, the key alterable genera in the GM associated with diabetes were identified as Blautia, Lactobacillus, Bacteroides, Prevotella, Faecalibacterium, Bifidobacterium, Ruminococcus, Clostridium, and Lachnoclostridium. The related metabolic pathways were identified as cholate degradation and L-histidine biosynthesis. Noteworthy, Blautia and Faecalibacterium displayed similar alterations in patients with IGT compared to those observed in patients with diabetes, and the GM metabolites, tauroursodeoxycholic acid (TUDCA) and carnosine (CARN, a downstream metabolite of histidine and alanine) were both found to be decreased, which in turn regulated the expression of proteins in plasma and mRNAs in neutrophils. Subsequent experiments focused on insulin-like growth factor-binding protein 3 and interleukin-6 due to their impact on blood glucose regulation and associated vascular inflammation. Both proteins were found to be suppressed by TUDCA and CARN in HepG2 cells and neutrophils.

CONCLUSION: Dysbiosis of the GM occurred throughout the entire progression from IGT to diabetes, characterized by an increase in Blautia and a decrease in Faecalibacterium, leading to reduced levels of TUDCA and CARN, which alleviated their inhibition on the expression of insulin-like growth factor-binding protein 3 and interleukin-6, contributing to the development of hyperglycemia and associated vasculopathy.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
*Carnosine/metabolism
Male
*Feces/microbiology
Glucose Intolerance/metabolism
Inflammation/metabolism
Hep G2 Cells
Metagenomics
Female
Middle Aged
Taurochenodeoxycholic Acid/metabolism/pharmacology
Hyperglycemia/metabolism
Neutrophils/metabolism
RNA, Ribosomal, 16S/genetics
Bacteria/classification/metabolism/genetics

@article {pmid39205200,
year = {2024},
author = {Santos, JPN and Rodrigues, GVP and Ferreira, LYM and Monteiro, GP and Fonseca, PLC and Lopes, ÍS and Florêncio, BS and da Silva Junior, AB and Ambrósio, PE and Pirovani, CP and Aguiar, ERGR},
title = {The Virome of Cocoa Fermentation-Associated Microorganisms.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/v16081226},
pmid = {39205200},
issn = {1999-4915},
support = {Financial code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (CAPES)/ ; Researcher fellowship//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; },
mesh = {*Cacao/virology/microbiology ; *Fermentation ; *Virome ; Viruses/genetics/classification/isolation & purification ; Fungi/virology/genetics/classification ; Phylogeny ; Bacteriophages/genetics/classification/isolation & purification ; Costa Rica ; Bacteria/genetics/classification/virology ; Metagenomics ; Genome, Viral ; },
abstract = {Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.},
}

*Cacao/virology/microbiology
*Fermentation
*Virome
Viruses/genetics/classification/isolation & purification
Fungi/virology/genetics/classification
Phylogeny
Bacteriophages/genetics/classification/isolation & purification
Costa Rica
Bacteria/genetics/classification/virology
Metagenomics
Genome, Viral

@article {pmid39202331,
year = {2024},
author = {Zheng, X and Xu, L and Tang, Q and Shi, K and Wang, Z and Shi, L and Ding, Y and Yin, Z and Zhang, X},
title = {Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/genes15080970},
pmid = {39202331},
issn = {2073-4425},
support = {202103a06020013//Major special science and technology project of Anhui Province/ ; GXXT-2023-059//the Cooperative Innovation Project of Anhui Provincial Universities/ ; 340000211260001000431//the Joint Research Project on Local Pig Breeding in Anhui Province/ ; 2021YFD1301200//National Key research and development Program of China/ ; },
mesh = {Animals ; *Weaning ; *Gastrointestinal Microbiome ; Swine ; *Metabolomics/methods ; *Metagenomics/methods ; Stress, Physiological ; Metabolome ; Animals, Newborn ; Cecum/microbiology/metabolism ; },
abstract = {(1) Background: Weaning is a challenging and stressful event in the pig's life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student's t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses-350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages.},
}

Animals
*Weaning
*Gastrointestinal Microbiome
Swine
*Metabolomics/methods
*Metagenomics/methods
Stress, Physiological
Metabolome
Animals, Newborn
Cecum/microbiology/metabolism

@article {pmid39201270,
year = {2024},
author = {Su, H and Yang, S and Chen, S and Chen, X and Guo, M and Zhu, L and Xu, W and Liu, H},
title = {What Happens in the Gut during the Formation of Neonatal Jaundice-Underhand Manipulation of Gut Microbiota?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168582},
pmid = {39201270},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Jaundice, Neonatal/therapy/microbiology/etiology ; Infant, Newborn ; *Probiotics ; *Bilirubin/metabolism/blood ; Breast Feeding ; Milk, Human/microbiology/metabolism ; },
abstract = {Jaundice is a symptom of high blood bilirubin levels affecting about 80% of neonates. In neonates fed with breast milk, jaundice is particularly prevalent and severe, which is likely multifactorial. With the development of genomics and metagenomics, a deeper understanding of the neonatal gut microbiota has been achieved. We find there are accumulating evidence to indicate the importance of the gut microbiota in the mechanism of jaundice. In this paper, we present new comprehensive insight into the relationship between the microbiota and jaundice. In the new perspective, the gut is a crucial crossroad of bilirubin excretion, and bacteria colonizing the gut could play different roles in the excretion of bilirubin, including Escherichia coli as the main traffic jam causers, some Clostridium and Bacteroides strains as the traffic police, and most probiotic Bifidobacterium and Lactobacillus strains as bystanders with no effect or only a secondary indirect effect on the metabolism of bilirubin. This insight could explain why breast milk jaundice causes a longer duration of blood bilirubin and why most probiotics have limited effects on neonatal jaundice. With the encouragement of breastmilk feeding, our perspective could guide the development of new therapy methods to prevent this side effect of breastfeeding.},
}

Humans
*Gastrointestinal Microbiome
*Jaundice, Neonatal/therapy/microbiology/etiology
Infant, Newborn
*Probiotics
*Bilirubin/metabolism/blood
Breast Feeding
Milk, Human/microbiology/metabolism

@article {pmid39201260,
year = {2024},
author = {Ryu, HM and Islam, SMS and Riaz, B and Sayeed, HM and Choi, B and Sohn, S},
title = {Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168571},
pmid = {39201260},
issn = {1422-0067},
mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Colitis/microbiology/therapy/diet therapy/chemically induced ; *Dextran Sulfate/toxicity ; RNA, Ribosomal, 16S/genetics ; Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy ; Biomarkers ; Mice, Inbred C57BL ; Colon/microbiology/pathology/metabolism ; },
abstract = {Ulcerative colitis (UC) is a persistent inflammatory intestinal disease that consistently affects the colon and rectum. Its exact cause remains unknown. UC causes a considerable challenge in healthcare, prompting research for novel therapeutic strategies. Although probiotics have gained popularity as possible candidates for managing UC, studies are still ongoing to identify the best probiotics or probiotic mixtures for clinical applications. This study aimed to determine the efficacy of a multi-strain probiotic mixture in mitigating intestinal inflammation in a colitis mouse model induced by dextran sulfate sodium. Specifically, a multi-strain probiotic mixture consisting of Tetragenococcus halophilus and Eubacterium rectale was used to study its impact on colitis symptoms. Anti-inflammatory effects were evaluated using ELISA and flow cytometry. The configuration of gut microbial communities was determined using 16S rRNA metagenomic analysis. According to this study, colitis mice treated with the probiotic mixture experienced reduced weight loss and significantly less colonic shortening compared to untreated mice. Additionally, the treated mice exhibited increased levels of forkhead box P3 (Foxp3) and interleukin 10, along with decreased expression of dendritic cell activation markers, such as CD40+, CD80+, and CD83+, in peripheral blood leukocytes and intraepithelial lymphocytes. Furthermore, there was a significant decrease in the frequencies of CD8+N.K1.1+ cells and CD11b+Ly6G+ cells. In terms of the gut microbiota, probiotic-mixture treatment of colitis mice significantly increased the abundance of the phyla Actinobacteria and Verrucomicrobia (p < 0.05). These results provide valuable insights into the therapeutic promise of multi-strain probiotics, shedding light on their potential to alleviate colitis symptoms. This research contributes to the ongoing exploration of effective probiotic interventions for managing inflammatory bowel disease.},
}

Animals
*Probiotics/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice
*Disease Models, Animal
*Colitis/microbiology/therapy/diet therapy/chemically induced
*Dextran Sulfate/toxicity
RNA, Ribosomal, 16S/genetics
Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy
Biomarkers
Mice, Inbred C57BL
Colon/microbiology/pathology/metabolism

@article {pmid39201258,
year = {2024},
author = {Al-Sarraj, F and Albiheyri, R and Qari, M and Alotaibi, M and Al-Zahrani, M and Anwar, Y and Alghamdi, MA and Nass, NM and Bouback, T and Alotibi, I and Radhwi, O and Sajer, BH and Redhwan, A and Al-Matary, MA and Almanzalawi, EA and Elshafie, HS},
title = {Genetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168570},
pmid = {39201258},
issn = {1422-0067},
support = {grant no. J: 007-130-1443.//Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah/ ; },
mesh = {Humans ; *Anemia, Sickle Cell/microbiology/genetics ; *Mouth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation & purification ; Young Adult ; Case-Control Studies ; Adolescent ; High-Throughput Nucleotide Sequencing ; Middle Aged ; },
abstract = {The Middle Eastern prevalence of sickle cell anemia, a genetic disorder that affects red blood cells, necessitates additional research. On a molecular level, we sought to identify and sort the oral microbiota of healthy individuals and those with sickle cell anemia. Furthermore, it is crucial to comprehend how changes in the genetic makeup of the oral microbiota impact the state of sickle cell anemia. Using next-generation sequencing, the 16S rRNA amplicon was examined using saliva samples from 36 individuals with sickle cell anemia and healthy individuals. These samples were obtained from sickle cell anemia patients (18 samples) and healthy control participants (controls, 18 samples). Various analyses are conducted using bioinformatic techniques to identify distinct species and their relative abundance. Streptococcus, followed by Fusobacterium nucleatum, Prevotella, and Veillonella were the most prevalent genera of bacteria in the saliva of the SCA and non-SCA individuals according to our findings. Rothia mucilaginosa, Prevotella scoposa, and Veillonella dispar species were the dominant species in both sickle cell anemia and non-sickle cell anemia subjects. Streptococcus salivarius, Actinomyces graevenitzii, Actinomyces odontolyticus, and Actinomyces georgiae spp. were the most prevalent bacterial spp. in the studied SCA cases. The sequencing of the 16S rRNA gene yielded relative abundance values that were visualized through a heatmap analysis. Alterations in the oral microflora's constitution can significantly affect the susceptibility of sickle cell anemia patients to develop more severe health complications. Salivary diagnosis is a potential tool for predicting and preventing oral microbiome-related diseases in the future.},
}

Humans
*Anemia, Sickle Cell/microbiology/genetics
*Mouth/microbiology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Female
Male
Adult
*Saliva/microbiology
Bacteria/genetics/classification/isolation & purification
Young Adult
Case-Control Studies
Adolescent
High-Throughput Nucleotide Sequencing
Middle Aged

@article {pmid39197040,
year = {2024},
author = {Chen, S and Zhang, Z and Liu, S and Chen, T and Lu, Z and Zhao, W and Mou, X and Liu, S},
title = {Consistent signatures in the human gut microbiome of longevous populations.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393756},
pmid = {39197040},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Longevity ; Aged, 80 and over ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Adult ; Male ; Aged ; Young Adult ; Metagenomics ; Middle Aged ; Desulfovibrio/genetics/metabolism ; },
abstract = {Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.},
}

Humans
*Gastrointestinal Microbiome
*Longevity
Aged, 80 and over
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Female
Adult
Male
Aged
Young Adult
Metagenomics
Middle Aged
Desulfovibrio/genetics/metabolism

@article {pmid39198832,
year = {2024},
author = {Su, W and Gong, C and Zhong, H and Yang, H and Chen, Y and Wu, X and Jin, J and Xi, H and Zhao, J},
title = {Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {22},
number = {1},
pages = {111},
pmid = {39198832},
issn = {1477-7827},
support = {437606312//Wenzhou Medical University advantageous and distinctive Discipline Construction Project/ ; },
mesh = {Humans ; Female ; *Embryo Transfer/methods ; *Dysbiosis/microbiology ; Adult ; *Vagina/microbiology ; *Microbiota/genetics/physiology ; *Endometrium/microbiology/metabolism ; *Embryo Implantation/physiology ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.

PURPOSE: This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.

METHODS: We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.

RESULTS: Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC = 0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.

CONCLUSIONS: This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.},
}

Humans
Female
*Embryo Transfer/methods
*Dysbiosis/microbiology
Adult
*Vagina/microbiology
*Microbiota/genetics/physiology
*Endometrium/microbiology/metabolism
*Embryo Implantation/physiology
Pregnancy
*Infertility, Female/microbiology/therapy
Fertilization in Vitro/methods
RNA, Ribosomal, 16S/genetics

@article {pmid39198826,
year = {2024},
author = {Su, Q and Zhuang, DH and Li, YC and Chen, Y and Wang, XY and Ge, MX and Xue, TY and Zhang, QY and Liu, XY and Yin, FQ and Han, YM and Gao, ZL and Zhao, L and Li, YX and Lv, MJ and Yang, LQ and Xia, TR and Luo, YJ and Zhang, Z and Kong, QP},
title = {Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {232},
pmid = {39198826},
issn = {1474-760X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Acclimatization ; *Altitude ; Animals ; Adult ; Male ; *Hypoxia/genetics ; Mice ; Female ; Longitudinal Studies ; Altitude Sickness/microbiology/genetics ; Middle Aged ; },
abstract = {BACKGROUND: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization.

RESULTS: To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress.

CONCLUSIONS: Our study underscores the importance of Blautia A species in the gut microbiota's rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.},
}

Humans
*Gastrointestinal Microbiome
*Acclimatization
*Altitude
Animals
Adult
Male
*Hypoxia/genetics
Mice
Female
Longitudinal Studies
Altitude Sickness/microbiology/genetics
Middle Aged

@article {pmid39198450,
year = {2024},
author = {Licht, P and Dominelli, N and Kleemann, J and Pastore, S and Müller, ES and Haist, M and Hartmann, KS and Stege, H and Bros, M and Meissner, M and Grabbe, S and Heermann, R and Mailänder, V},
title = {The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {74},
pmid = {39198450},
issn = {2055-5008},
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; Female ; Middle Aged ; Male ; *Staphylococcus aureus/genetics/pathogenicity/isolation & purification ; *Lymphoma, T-Cell, Cutaneous/microbiology ; Aged ; *Mycosis Fungoides/microbiology ; Dysbiosis/microbiology ; Skin Neoplasms/microbiology/pathology ; Adult ; Aged, 80 and over ; Metagenomics/methods ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.},
}

Humans
*Microbiota
*Skin/microbiology
Female
Middle Aged
Male
*Staphylococcus aureus/genetics/pathogenicity/isolation & purification
*Lymphoma, T-Cell, Cutaneous/microbiology
Aged
*Mycosis Fungoides/microbiology
Dysbiosis/microbiology
Skin Neoplasms/microbiology/pathology
Adult
Aged, 80 and over
Metagenomics/methods
Virulence Factors/genetics
Bacteria/classification/genetics/isolation & purification

@article {pmid39198444,
year = {2024},
author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J},
title = {Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7447},
pmid = {39198444},
issn = {2041-1723},
support = {UL1TR002377//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Feces/microbiology ; *Health Status ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; Female ; },
abstract = {Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Feces/microbiology
*Health Status
Metagenome
Bacteria/classification/genetics/isolation & purification
Female

@article {pmid39198442,
year = {2024},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7450},
pmid = {39198442},
issn = {2041-1723},
support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Feces/microbiology ; *Escherichia coli/genetics/isolation & purification ; Humans ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Nanopores ; Escherichia coli Proteins/genetics ; Plasmids/genetics ; Nanopore Sequencing/methods ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; },
abstract = {The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.},
}

*Feces/microbiology
*Escherichia coli/genetics/isolation & purification
Humans
*beta-Lactamases/genetics/metabolism
*Metagenomics/methods
*Nanopores
Escherichia coli Proteins/genetics
Plasmids/genetics
Nanopore Sequencing/methods
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/genetics

@article {pmid39198293,
year = {2024},
author = {Joseph, B and Babu, S},
title = {Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {331},
pmid = {39198293},
issn = {1432-0991},
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Helianthus/microbiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Plant Leaves/microbiology ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification ; *Manure/microbiology ; Microbiota ; Biodiversity ; Metagenomics ; },
abstract = {Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.},
}

*Fertilizers/analysis
*Rhizosphere
*Helianthus/microbiology
*Bacteria/classification/genetics/isolation & purification/drug effects
*Plant Leaves/microbiology
*Soil Microbiology
*Fungi/classification/genetics/isolation & purification
*Manure/microbiology
Microbiota
Biodiversity
Metagenomics

@article {pmid39127317,
year = {2024},
author = {Tang, W and Wang, Q and Sun, M and Liu, C and Huang, Y and Zhou, M and Zhang, X and Meng, Z and Zhang, J},
title = {The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders.},
journal = {Life sciences},
volume = {354},
number = {},
pages = {122952},
doi = {10.1016/j.lfs.2024.122952},
pmid = {39127317},
issn = {1879-0631},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Oligodendroglia/metabolism ; *Homeostasis/physiology ; *Demyelinating Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Myelin Sheath/metabolism ; },
abstract = {The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
*Oligodendroglia/metabolism
*Homeostasis/physiology
*Demyelinating Diseases/metabolism/microbiology
*Brain-Gut Axis/physiology
Dysbiosis/microbiology
Myelin Sheath/metabolism

@article {pmid39110597,
year = {2024},
author = {Fu, Y and Yu, S and Li, J and Lao, Z and Yang, X and Lin, Z},
title = {DeepMineLys: Deep mining of phage lysins from human microbiome.},
journal = {Cell reports},
volume = {43},
number = {8},
pages = {114583},
doi = {10.1016/j.celrep.2024.114583},
pmid = {39110597},
issn = {2211-1247},
mesh = {Humans ; *Microbiota ; *Bacteriophages/genetics/metabolism ; Data Mining ; Viral Proteins/metabolism ; Neural Networks, Computer ; Animals ; Muramidase/metabolism ; Escherichia coli/genetics/metabolism ; },
abstract = {Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.},
}

Humans
*Microbiota
*Bacteriophages/genetics/metabolism
Data Mining
Viral Proteins/metabolism
Neural Networks, Computer
Animals
Muramidase/metabolism
Escherichia coli/genetics/metabolism

@article {pmid38986824,
year = {2024},
author = {de Deus, DR and Siqueira, JAM and Maués, MAC and de Fátima Mesquita de Figueiredo, MJ and Júnior, ECS and da Silva Bandeira, R and da Costa Pinheiro, K and Teixeira, DM and da Silva, LD and de Fátima Dos Santos Guerra, S and da Silva Soares, L and Gabbay, YB},
title = {Analysis of viral diversity in dogs with acute gastroenteritis from Brazilian Amazon.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {123},
number = {},
pages = {105637},
doi = {10.1016/j.meegid.2024.105637},
pmid = {38986824},
issn = {1567-7257},
mesh = {Dogs ; Animals ; *Gastroenteritis/virology/veterinary/epidemiology ; Brazil/epidemiology ; *Dog Diseases/virology/epidemiology ; *Phylogeny ; Norovirus/genetics/classification/isolation & purification ; Feces/virology ; Genome, Viral ; Genetic Variation ; Metagenomics/methods ; Viruses/classification/genetics/isolation & purification ; Virome ; },
abstract = {Viral gastroenteritis is commonly reported in dogs and involves a great diversity of enteric viruses. In this research, viral diversity was investigated in dogs with diarrhea in Northern Brazil using shotgun metagenomics. Furthermore, the presence of norovirus (NoV) was investigated in 282 stool/rectal swabs of young/adult dogs with or without diarrhea from two public kennels, based on one-step reverse transcription polymerase chain reaction (RT-PCR) for genogroup VI and VII (GVI and GVII) and real-time RT-PCR for GI, GII, and GIV. Thirty-one viral families were identified, including bacteriophages. Phylogenetic analyses showed twelve complete or nearly complete genomes belonging to the species of Protoparvovirus carnivoran1, Mamastrovirus 5, Aichivirus A2, Alphacoronavirus 1, and Chipapillomavirus 1. This is the first description of the intestinal virome of dogs in Northern Brazil and the first detection of canine norovirus GVII in the country. These results are important for helping to understand the viral groups that circulate in the canine population.},
}

Dogs
Animals
*Gastroenteritis/virology/veterinary/epidemiology
Brazil/epidemiology
*Dog Diseases/virology/epidemiology
*Phylogeny
Norovirus/genetics/classification/isolation & purification
Feces/virology
Genome, Viral
Genetic Variation
Metagenomics/methods
Viruses/classification/genetics/isolation & purification
Virome

@article {pmid38964747,
year = {2024},
author = {Łukasik, J and Dierikx, T and Johnston, BC and de Meij, T and Szajewska, H},
title = {Systematic review: effect of probiotics on antibiotic-induced microbiome disruption.},
journal = {Beneficial microbes},
volume = {15},
number = {5},
pages = {431-447},
doi = {10.1163/18762891-bja00023},
pmid = {38964747},
issn = {1876-2891},
mesh = {*Probiotics/pharmacology/administration & dosage ; Humans ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Dysbiosis/microbiology ; Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effectiveness of probiotics in preventing or reversing antibiotic-induced microbiome disruption remains uncertain, and claims of microbiome restoration to its pre-antibiotic state may be overestimated. In this review, we aimed to assess the efficacy of probiotics in preventing or ameliorating disruptions in microbiome composition and function induced by antibiotic treatment. We searched Medline, Embase, and CENTRAL for randomised controlled and non-randomised trials. Participants were individuals of any age who were on systemic antibiotics with a low risk of baseline dysbiosis. The intervention consisted of probiotics during or after antibiotic treatment, compared to placebo, alternative interventions, or no intervention. Outcomes included microbiome composition and diversity analysed using high-throughput molecular methods, alongside microbial function and resistome assessments. Seven studies, reported in eight papers, were reviewed. One study showed probiotics counteracting antibiotic-induced diversity changes, another showed exacerbation of these changes, and four others showed no effect. Effects on taxa abundance ranged from mitigating dysbiosis to selective modulation, no effect, or delayed recovery. One study observed no impact on the resistome, while another reported an increase in antibiotic resistance genes. In conclusion, heterogeneous results preclude a definitive conclusion on the effectiveness of any specific probiotic in restoring antibiotic-exposed microbiomes. For a clearer understanding, future research should be more standardised and long-term, employing advanced methods, such as 16S rRNA gene sequencing and metagenomic sequencing. These studies should strive to include larger, diverse populations to enhance generalisability and clearly define what constitutes a healthy microbiome. Finally, linking changes in the microbiome to specific clinical outcomes is essential for clinical decision making. PROSPERO registration number: CRD42023446214.},
}

*Probiotics/pharmacology/administration & dosage
Humans
*Anti-Bacterial Agents/pharmacology/adverse effects
*Dysbiosis/microbiology
Microbiota/drug effects
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid38960356,
year = {2024},
author = {Zhang, W and Ye, J and Hu, F and Zhang, J and Chen, P and Yuan, Z and Xu, Z},
title = {Microbial community succession and responses to internal environmental drivers throughout the operation of constructed wetlands.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119522},
doi = {10.1016/j.envres.2024.119522},
pmid = {38960356},
issn = {1096-0953},
mesh = {*Wetlands ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; },
abstract = {Constructed wetlands (CWs) have been widely used to ensure effective domestic wastewater treatment. Microorganisms-derived CWs have received extensive attention as they play a crucial role. However, research on the succession patterns of microbial communities and the influencing mechanisms of internal environmental factors throughout entire CW operations remains limited. In this context, three parallel-operated CWs were established in this study to assess the microbial communities and their influencing environmental factors at different substrate depths throughout the operation process using 16S rRNA gene high-throughput sequencing and metagenomic sequencing. The results showed gradual reproduction and accumulation of the microbial communities throughout the CW operation. Although gradual increases in the richness and diversity of the microbial communities were found, there were decreases in the functional expression of the dominant microbial species. The excessive accumulation of microorganisms will decrease the oxidation-reduction potential (ORP) within CWs and attenuate their influence on effluent. Dissolved oxygen (DO) was the major factor influencing the microbial community succession over the CW operation. The main identified functional bacterial genera responsible for the ammonium oxidation, nitrification, and denitrification processes in the CWs were Nitrosospira, Nitrobacter, Nitrospira, Rhodanobacter, and Nakamurella. The narG gene was identified as a key functional gene linking various components of nitrogen cycling, while pH, electrical conductivity (EC), and ORP were the major environmental factors affecting the metabolism characteristics of nitrogen functional microorganisms. This study provides a theoretical basis for the effective regulation of related microbial communities to achieve long-term, efficient, and stable CW operations.},
}

*Wetlands
*Microbiota
RNA, Ribosomal, 16S/genetics
Waste Disposal, Fluid/methods
Bacteria/genetics/classification/isolation & purification/metabolism

@article {pmid39195462,
year = {2024},
author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y},
title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.},
journal = {Marine drugs},
volume = {22},
number = {8},
pages = {},
doi = {10.3390/md22080346},
pmid = {39195462},
issn = {1660-3397},
support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; },
mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; },
abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.},
}

*Chitin/chemistry
Animals
*Oligosaccharides/chemistry
*Microbiota
*Chitinases/metabolism
*Animal Shells/chemistry
Metagenomics/methods
Temperature
Polymerization
Bacteria

@article {pmid39192682,
year = {2024},
author = {Flynn, PJ and Moreau, CS},
title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17519},
doi = {10.1111/mec.17519},
pmid = {39192682},
issn = {1365-294X},
support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; },
abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.},
}

@article {pmid39192352,
year = {2024},
author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L},
title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.},
journal = {Hereditas},
volume = {161},
number = {1},
pages = {26},
pmid = {39192352},
issn = {1601-5223},
support = {No. 2023349//Chengdu Municipal Health Commission/ ; },
mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.

METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.

RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.

CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.},
}

*Carcinoma, Non-Small-Cell Lung/genetics
Humans
*Gastrointestinal Microbiome
*Lung Neoplasms/genetics/microbiology
Male
Middle Aged
Female
Feces/microbiology
Aged
Metagenome
Metagenomics/methods
Bacteria/genetics/classification

@article {pmid39192220,
year = {2024},
author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S},
title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {315},
pmid = {39192220},
issn = {1471-2180},
support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; },
mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation & purification ; },
abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.},
}

*Porifera/microbiology
Animals
Indian Ocean
*Metagenomics
*Microbiota/genetics
Egypt
Bacteria/genetics/classification
Phylogeny
Biodiversity
Multigene Family
Biological Products/metabolism
Metagenome
Proteobacteria/genetics/classification/isolation & purification

@article {pmid39113195,
year = {2024},
author = {Dong, T and Wang, Y and Qi, C and Fan, W and Xie, J and Chen, H and Zhou, H and Han, X},
title = {Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {8},
pages = {1617-1626},
doi = {10.4014/jmb.2402.02004},
pmid = {39113195},
issn = {1738-8872},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics/drug effects ; Retrospective Studies ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests ; Respiratory Tract Infections/microbiology/drug therapy ; Genes, Bacterial/genetics ; Male ; Female ; Middle Aged ; },
abstract = {Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Microbiota/genetics/drug effects
Retrospective Studies
*Drug Resistance, Bacterial/genetics
Metagenomics/methods
Microbial Sensitivity Tests
Respiratory Tract Infections/microbiology/drug therapy
Genes, Bacterial/genetics
Male
Female
Middle Aged

@article {pmid38807549,
year = {2024},
author = {Bae, WY and Jung, WH and Shin, SL and Kim, TR and Sohn, M and Suk, J and Jung, I and Lee, YI and Lee, JH},
title = {Heat-treated Limosilactobacillus fermentum LM1020 with menthol, salicylic acid, and panthenol promotes hair growth and regulates hair scalp microbiome balance in androgenetic alopecia: A double-blind, randomized and placebo-controlled clinical trial.},
journal = {Journal of cosmetic dermatology},
volume = {23},
number = {9},
pages = {2943-2955},
doi = {10.1111/jocd.16357},
pmid = {38807549},
issn = {1473-2165},
support = {S3003957//Ministry of SMEs and Startups/ ; },
mesh = {Humans ; *Alopecia/therapy/microbiology/drug therapy ; Double-Blind Method ; *Scalp/microbiology ; *Microbiota/drug effects ; Adult ; *Limosilactobacillus fermentum/physiology/isolation & purification ; Male ; Female ; Hair/microbiology/growth & development ; Middle Aged ; Hair Follicle/microbiology ; Hot Temperature ; Cell Proliferation/drug effects ; },
abstract = {BACKGROUND: Androgenetic alopecia (AGA) is a common and chronic problem characterized by hair follicle miniaturization.

AIMS: In this study, heat-treated Limosilactobacillus fermentum LM1020 (HT-LM1020) was investigated in human follicle dermal papilla cell (HFDPC), scalp tissue, and clinical trials for patients with AGA.

PATIENTS/METHODS: Cell proliferation and the expression of cyclins and cyclin-dependent kinases (CDKs) were measured in HFDPC. The relative gene expression of 5α-reductase and growth factors were investigated in hair scalp. This double-blind, randomized, placebo-controlled clinical trial was conducted over 24 weeks. Primary efficacy was evaluated by measuring hair density, and secondary efficacy was assessed by experts and self-assessment. Changes in the microbiota of the hair scalps were analyzed using 16S metagenome amplicon sequencing.

RESULTS: HT-LM1020 promoted cell growth (p < 0.001) and cyclin B1 expression, and it reduced 5α-reductase and induced fibroblast growth factor 7 (FGF7), FGF10, and epithelial growth factor7 (EGF7) (p < 0.001). In the clinical trial, the experimental group demonstrated an increase in hair density from 133.70 to 148.87 n/cm[2] at Week 24 (p < 0.001), while also expressing satisfaction with their hair density, reduced hair loss, and hairline. At Week 24, the total ratio of lactic acid bacteria operational taxonomic unit (OTU) in the scalp increased from 6.65% to 26.19%. At the same period, placebo-controlled group decreased Staphylococcus caprae OTU from 77.95% to 14.57% while experimental group decreased from 65.80% to 41.02%.

CONCLUSIONS: These present results showed that HT-LM1020 was a co-effector of ingredients for anti-hair loss contributing to cell proliferation and the expression of CDKs.},
}

Humans
*Alopecia/therapy/microbiology/drug therapy
Double-Blind Method
*Scalp/microbiology
*Microbiota/drug effects
Adult
*Limosilactobacillus fermentum/physiology/isolation & purification
Male
Female
Hair/microbiology/growth & development
Middle Aged
Hair Follicle/microbiology
Hot Temperature
Cell Proliferation/drug effects

@article {pmid39191812,
year = {2024},
author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H},
title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {72},
pmid = {39191812},
issn = {2055-5008},
mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; },
abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.},
}

Animals
*Host Specificity
*Bacteriophages/genetics/physiology
*Gastrointestinal Microbiome
Bees/virology/microbiology
*Bacteria/virology/genetics/classification
*Phylogeny
Metagenomics/methods
Metagenome

@article {pmid39191760,
year = {2024},
author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R},
title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {73},
pmid = {39191760},
issn = {2055-5008},
support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.},
}

*Irritable Bowel Syndrome/therapy/microbiology
Humans
*Fecal Microbiota Transplantation/methods
*RNA, Ribosomal, 16S/genetics
Female
Male
Adult
Treatment Outcome
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification

@article {pmid39189742,
year = {2024},
author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C},
title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.},
journal = {mBio},
volume = {},
number = {},
pages = {e0204424},
doi = {10.1128/mbio.02044-24},
pmid = {39189742},
issn = {2150-7511},
abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.},
}

@article {pmid39189169,
year = {2024},
author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD},
title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.},
journal = {Journal of xenobiotics},
volume = {14},
number = {3},
pages = {970-988},
doi = {10.3390/jox14030054},
pmid = {39189169},
issn = {2039-4713},
support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.},
}

@article {pmid39187802,
year = {2024},
author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH},
title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1001},
pmid = {39187802},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation & purification ; Aged ; },
abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.

METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).

RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.

CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.

TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.},
}

Humans
*Microbiota
*Biofilms
*Gingival Crevicular Fluid/microbiology
*Dental Implants/microbiology
Middle Aged
Specimen Handling/methods
Female
Male
High-Throughput Nucleotide Sequencing
Bacteria/classification/isolation & purification
Aged

@article {pmid39185682,
year = {2024},
author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES},
title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2394248},
doi = {10.1080/19490976.2024.2394248},
pmid = {39185682},
issn = {1949-0984},
mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Longitudinal Studies ; },
abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.},
}

Humans
Female
*COVID-19/microbiology/virology
*HIV Infections/microbiology/virology
*Virome
*Gastrointestinal Microbiome
*SARS-CoV-2/genetics/isolation & purification
Adult
Infant, Newborn
*Feces/microbiology/virology
Infant
Bacteria/classification/isolation & purification/genetics
Longitudinal Studies

@article {pmid39120615,
year = {2024},
author = {Li, X and Tao, Q and Hu, Q and Ma, N and Ma, G},
title = {In vitro gastrointestinal digestion and fecal fermentation of Pleurotus eryngii proteins extracted using different methods: insights for the utilization of edible mushroom-based proteins as novel nutritional and functional components.},
journal = {Food & function},
volume = {15},
number = {17},
pages = {8865-8877},
doi = {10.1039/d4fo02604g},
pmid = {39120615},
issn = {2042-650X},
mesh = {*Pleurotus/metabolism/chemistry ; *Digestion ; *Fermentation ; *Feces/microbiology ; *Fungal Proteins/metabolism ; Humans ; Gastrointestinal Tract/metabolism/microbiology ; Gastrointestinal Microbiome ; Hydrolysis ; },
abstract = {Pleurotus eryngii (P. eryngii) protein is considered a high-quality protein because it is rich in essential amino acids and displays multiple significant functional characterizations that vary with its fabrication processes. We aimed to investigate the differences in P. eryngii protein extracted via alkaline extraction and acid precipitation (AA), cellulase complex alkaline extraction and acid precipitation (CAA), ultrasound-assisted alkaline extraction and acid precipitation (UAA), and salt dissolution (S) in terms of gastrointestinal digestion and fecal fermentation consequences. Protein hydrolysis and structural analysis were performed after in vitro gastrointestinal digestion, and it was found that AA showed the highest hydrolysis degree, whereas CAA showed the lowest. The results of fluorescence chromatography and infrared chromatography indicated that the reasons for the digestion difference might be the unfolding degrees of the protein tertiary structure and polysaccharide content, which is the major component of crude proteins and can prevent protein hydrolysis. Metagenomic analysis suggested that compared with other groups, AA had excellent biological functions, including regulating obesity and insulin-related microbiota. This study could provide a new theoretical basis for the P. eryngii protein as a novel type of nutritional and functional component and contributes to the development of a diversified emerging food protein supply system.},
}

*Pleurotus/metabolism/chemistry
*Digestion
*Fermentation
*Feces/microbiology
*Fungal Proteins/metabolism
Humans
Gastrointestinal Tract/metabolism/microbiology
Gastrointestinal Microbiome
Hydrolysis

@article {pmid39117202,
year = {2024},
author = {Tariq, M and Liu, Y and Rizwan, A and Shoukat, CA and Aftab, Q and Lu, J and Zhang, Y},
title = {Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175354},
doi = {10.1016/j.scitotenv.2024.175354},
pmid = {39117202},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Nitrogen/metabolism ; *Carbon Dioxide/metabolism ; *Microbiota ; *Carbon/metabolism ; Climate Change ; Soil/chemistry ; Carbon Cycle ; },
abstract = {In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.},
}

*Soil Microbiology
*Nitrogen/metabolism
*Carbon Dioxide/metabolism
*Microbiota
*Carbon/metabolism
Climate Change
Soil/chemistry
Carbon Cycle

@article {pmid39111416,
year = {2024},
author = {Wang, HY and Yu, ZG and Zhou, FW and Hernandez, JC and Grandjean, A and Biester, H and Xiao, KQ and Knorr, KH},
title = {Microbial communities and functions are structured by vertical geochemical zones in a northern peatland.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175273},
doi = {10.1016/j.scitotenv.2024.175273},
pmid = {39111416},
issn = {1879-1026},
mesh = {*Microbiota ; China ; *Soil Microbiology ; *Methane/metabolism/analysis ; RNA, Ribosomal, 16S ; Soil/chemistry ; Wetlands ; Carbon/analysis ; Nitrogen/analysis ; Bacteria/classification ; Sulfur/metabolism/analysis ; Archaea/classification ; },
abstract = {Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L[-1]. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm[-3]·d[-1], while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.},
}

*Microbiota
China
*Soil Microbiology
*Methane/metabolism/analysis
RNA, Ribosomal, 16S
Soil/chemistry
Wetlands
Carbon/analysis
Nitrogen/analysis
Bacteria/classification
Sulfur/metabolism/analysis
Archaea/classification

@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}

Animals
*Plasmids/genetics
China
*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Farms
Drug Resistance, Bacterial/genetics
Rana catesbeiana/microbiology/genetics
Drug Resistance, Microbial/genetics
Microbiota/genetics

@article {pmid39082382,
year = {2024},
author = {Vidal-Villarejo, M and Dößelmann, B and Kogler, B and Hammerschmidt, M and Oppliger, B and Oppliger, H and Schmid, K},
title = {Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis.},
journal = {Molecular ecology},
volume = {33},
number = {17},
pages = {e17482},
doi = {10.1111/mec.17482},
pmid = {39082382},
issn = {1365-294X},
support = {SCHM 1354-11/1//Deutsche Forschungsgemeinschaft/ ; 031B0731A//Bundesministerium für Bildung und Forschung/ ; PGRL-NN-0061//Swiss National Action Plan NAP-PGREL/ ; },
mesh = {*Zea mays/microbiology ; Switzerland ; *Ascomycota/genetics ; *Plant Leaves/microbiology ; *Plant Diseases/microbiology ; *Microbiota/genetics ; *Metagenomics ; },
abstract = {The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.},
}

*Zea mays/microbiology
Switzerland
*Ascomycota/genetics
*Plant Leaves/microbiology
*Plant Diseases/microbiology
*Microbiota/genetics
*Metagenomics

@article {pmid39056112,
year = {2024},
author = {Dong, J and Zhang, J and Cheng, S and Qin, B and Jin, K and Chen, B and Zhang, Y and Lu, J},
title = {A high-fat diet induced depression-like phenotype via hypocretin-HCRTR1 mediated inflammation activation.},
journal = {Food & function},
volume = {15},
number = {17},
pages = {8661-8673},
doi = {10.1039/d4fo00210e},
pmid = {39056112},
issn = {2042-650X},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Mice ; Rats ; *Depression/metabolism ; *Rats, Sprague-Dawley ; *Mice, Inbred C57BL ; *Inflammation/metabolism ; *Orexins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Orexin Receptors/metabolism/genetics ; Hippocampus/metabolism/drug effects ; 3T3-L1 Cells ; Microglia/metabolism/drug effects ; Phenotype ; Benzoxazoles ; Naphthyridines ; Urea/analogs & derivatives ; },
abstract = {Background: A high-fat diet (HFD) is generally associated with an increased risk of mental disorders that constitute a sizeable worldwide health. A HFD results in the gut microbiota-brain axis being altered and linked to mental disorders. Hypocretin-1, which can promote appetite, has been previously confirmed to be associated with depression. However, no exact relationship has been found for hypocretin between depression and HFDs. Methods: Adult male SD rats were randomly assigned to either a HFD or a normal diet for eight weeks, followed by behavioral tests and plasma biochemical analyses. Then, we investigated the protein and mRNA levels of inflammation-related factors in the hippocampus. We also observed morphological changes in brain microglia and lipid accumulation. Additionally, metagenomic and metabolomic analyses of gut microbiomes were performed. 3T3-L1 cells were utilized in vitro to investigate the impact of hypocretin receptor 1 antagonists (SB334867) on lipid accumulation. To consider the connection between the brain and adipose tissue, we used a conditioned medium (CM) treated with 3T3-L1 cells to observe the activation and phagocytosis of BV2 cells. Following a 12-week period of feeding a HFD to C57BL/6 mice, a three-week intervention period was initiated during which the administration of SB334867 was observed. This was followed by a series of assessments, including monitoring of body weight changes and emotional problems, as well as attention to plasma biochemical levels and microglial cell phenotypes in the brain. Results: The HFD rats displayed anxiety and depressive-like behaviors. HFD rats exhibited increased plasma HDL, LDL, and TC levels. A HFD also causes an increase in hypocretin-1 and hypocretin-2 in the hypothalamus. Metagenomics and metabolomics revealed that the HFD caused an increase in the relative abundance of associated inflammatory bacteria and decreased the abundance of anti-inflammatory and bile acid metabolites. Compared with the CTR group, hippocampal microglia in the HFD group were significantly activated and accompanied by lipid deposition. At the same time, protein and mRNA expression levels of inflammation-related factors were increased. We found that SB334867 could significantly reduce lipid accumulation in 3T3-L1 cells after differentiation. The expression of inflammatory factors decreased in the SB334867 group. The administration of SB334867 was found to reverse the adverse effects of the HFD on body weight, depressive-like behaviour and anxiety-like mood. Furthermore, this treatment was associated with improvements in plasma biochemical levels and a reduction in the number of microglia in the brain. Conclusions: In summary, our results demonstrated that a HFD induced anxiety and depressive-like behaviors, which may be linked to the increased hypocretin-1 level and lipid accumulation. Supplementation with SB334867 improved the above. These observations highlight the possibility of hypocretin-1 inducing the risk of HFD-associated emotional dysfunctions.},
}

Animals
*Diet, High-Fat/adverse effects
Male
Mice
Rats
*Depression/metabolism
*Rats, Sprague-Dawley
*Mice, Inbred C57BL
*Inflammation/metabolism
*Orexins/metabolism
*Gastrointestinal Microbiome/drug effects
*Orexin Receptors/metabolism/genetics
Hippocampus/metabolism/drug effects
3T3-L1 Cells
Microglia/metabolism/drug effects
Phenotype
Benzoxazoles
Naphthyridines
Urea/analogs & derivatives

@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {34},
number = {9},
pages = {3420-3433},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; R35GM133510/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Feces/microbiology ; Pilot Projects ; Male ; Female ; Cross-Sectional Studies ; Case-Control Studies ; Middle Aged ; *Bariatric Surgery ; *Bile Acids and Salts/metabolism ; Adult ; *Obesity, Morbid/surgery/microbiology ; Gastrointestinal Microbiome/physiology ; Weight Loss ; Lithocholic Acid/metabolism ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}

Humans
*Feces/microbiology
Pilot Projects
Male
Female
Cross-Sectional Studies
Case-Control Studies
Middle Aged
*Bariatric Surgery
*Bile Acids and Salts/metabolism
Adult
*Obesity, Morbid/surgery/microbiology
Gastrointestinal Microbiome/physiology
Weight Loss
Lithocholic Acid/metabolism

@article {pmid38996003,
year = {2024},
author = {Byndloss, M and Devkota, S and Duca, F and Hendrik Niess, J and Nieuwdorp, M and Orho-Melander, M and Sanz, Y and Tremaroli, V and Zhao, L},
title = {The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum.},
journal = {Diabetes care},
volume = {47},
number = {9},
pages = {1491-1508},
doi = {10.2337/dci24-0052},
pmid = {38996003},
issn = {1935-5548},
support = {//Novo Nordisk/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology ; Diabetes Mellitus/microbiology ; },
abstract = {This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 2/microbiology
Diabetes Mellitus/microbiology

@article {pmid38990271,
year = {2024},
author = {Ulger, Y and Delik, A and Akkız, H},
title = {Gut Microbiome and colorectal cancer: discovery of bacterial changes with metagenomics application in Turkısh population.},
journal = {Genes & genomics},
volume = {46},
number = {9},
pages = {1059-1070},
pmid = {38990271},
issn = {2092-9293},
support = {148-TGD-2022//Turkish Gastroenterology Association/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Female ; Male ; *Metagenomics/methods ; Aged ; Turkey ; Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the 3rd most common cancer in the world and colonic carcinogenesis is a multifactorial disease that involves environmental and genetic factors. Gut microbiota plays a critical role in the regulation of intestinal homeostasis. Increasing evidence shows that the gut microbiome plays a role in CRC development and may be a biomarker for early diagnosis.

OBJECTIVE: This study aimed to determine the clinical prognostic significance of gut microbiota in CRC patients in the Turkish population by metagenomic analysis and to determine the microbial composition in tumor tissue biopsy samples.

METHODS: Tissue biopsies were taken from the participants with sterile forceps during colonoscopy and stored at -80 °C. Then, DNA isolation was performed from the tissue samples and the V3-V4 region of the 16 S rRNA gene was sequenced on the Illumina MiSeq platform. Quality control of the obtained sequence data was performed. Operational taxonomic units (OTUs) were classified according to the Greengenes database. Alpha diversity (Shannon index) and beta diversity (Bray-Curtis distance) analyses were performed. The most common bacterial species in CRC patients and healthy controls were determined and whether there were statistically significant differences between the groups was tested.

RESULTS: A total of 40 individuals, 13 CRC patients and 20 healthy control individuals were included in our metagenomic study. The mean age of the patients was 64.83 and BMI was 25.85. In CRC patients, the level of Bacteroidetes at the phylum taxonomy was significantly increased (p = 0.04), the level of Clostridia at the class taxonomy was increased (p = 0.23), and the level of Enterococcus at the genus taxonomy was significantly increased (p = 0.01). When CRC patients were compared with the control group, significant increases were detected in the species of Gemmiger formicilis (p = 0.15), Prevotella copri (p = 0.02) and Ruminococcus bromii (p = 0.001) at the species taxonomy.

CONCLUSIONS: Metagenomic analysis of intestinal microbiota composition in CRC patients provides important data for determining the treatment options for these patients. The results of this study suggest that it may be beneficial in terms of early diagnosis, poor prognosis and survival rates in CRC patients. In addition, this metagenomic study is the first study on the colon microbiome associated with CRC mucosa in the Turkish population.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics/pathology
*Gastrointestinal Microbiome/genetics
Middle Aged
Female
Male
*Metagenomics/methods
Aged
Turkey
Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid39185088,
year = {2024},
author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L},
title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1369192},
doi = {10.3389/fcimb.2024.1369192},
pmid = {39185088},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; },
abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.

METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.

RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-α levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.

CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.},
}

Humans
Female
Pregnancy
*Hypothyroidism/microbiology
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Adult
*Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Pregnancy Complications/microbiology
Metagenome
Feces/microbiology

@article {pmid39185086,
year = {2024},
author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W},
title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1410681},
doi = {10.3389/fcimb.2024.1410681},
pmid = {39185086},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; },
abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.

METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.

RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).

CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
*Microbiota
Middle Aged
*Bronchoalveolar Lavage Fluid/microbiology
Retrospective Studies
Aged
Lung/microbiology/pathology/diagnostic imaging
High-Throughput Nucleotide Sequencing
Adult
Respiratory System/microbiology
Metagenomics/methods
Risk Factors

@article {pmid39182301,
year = {2024},
author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C},
title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135567},
doi = {10.1016/j.jhazmat.2024.135567},
pmid = {39182301},
issn = {1873-3336},
abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.},
}

@article {pmid39182227,
year = {2024},
author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS},
title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2389319},
doi = {10.1080/19490976.2024.2389319},
pmid = {39182227},
issn = {1949-0984},
mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; },
abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.},
}

Animals
*Butyrates/metabolism
*Gastrointestinal Microbiome
Mice
*Alzheimer Disease/microbiology/pathology/metabolism
*Memory Disorders/microbiology/metabolism/pathology
*Bacteria/classification/metabolism/genetics/isolation & purification
*Disease Models, Animal
*Dysbiosis/microbiology
Hippocampus/metabolism/pathology
Mice, Transgenic
Male
Disease Progression
Brain-Gut Axis/physiology
Brain/metabolism/pathology

@article {pmid39182035,
year = {2024},
author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L},
title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {313},
pmid = {39182035},
issn = {1471-2180},
mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; },
abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.

RESULTS: At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.

CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.},
}

*Bioreactors/microbiology
*Zinc/metabolism
*Nickel/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Metagenomics
*Copper/metabolism
*Biodiversity
Wastewater/microbiology/chemistry

@article {pmid39180208,
year = {2024},
author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y},
title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.},
journal = {Critical reviews in eukaryotic gene expression},
volume = {34},
number = {8},
pages = {59-73},
pmid = {39180208},
issn = {1045-4403},
mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.},
}

Humans
Female
*Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Milk, Human/microbiology
Infant
Infant, Newborn
Intestines/microbiology
Male
Drug Resistance, Bacterial/genetics
Genes, Bacterial
Gastrointestinal Microbiome/genetics/drug effects
Bacteria/genetics/drug effects
Drug Resistance, Microbial/genetics

@article {pmid39127363,
year = {2024},
author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T},
title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.},
journal = {Bioresource technology},
volume = {409},
number = {},
pages = {131244},
doi = {10.1016/j.biortech.2024.131244},
pmid = {39127363},
issn = {1873-2976},
mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; },
abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.},
}

*Hydrocarbons/metabolism
*Biodegradation, Environmental
*Oil and Gas Fields/microbiology
Microbial Consortia/physiology
Bacteria/metabolism
Petroleum/metabolism
Phylogeny

@article {pmid39122016,
year = {2024},
author = {Fiorucci, S and Marchianò, S and Urbani, G and Di Giorgio, C and Distrutti, E and Zampella, A and Biagioli, M},
title = {Immunology of bile acids regulated receptors.},
journal = {Progress in lipid research},
volume = {95},
number = {},
pages = {101291},
doi = {10.1016/j.plipres.2024.101291},
pmid = {39122016},
issn = {1873-2194},
mesh = {Humans ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Gastrointestinal Microbiome/immunology ; },
abstract = {Bile acids are steroids formed at the interface of host metabolism and intestinal microbiota. While primary bile acids are generated in the liver from cholesterol metabolism, secondary bile acids represent the products of microbial enzymes. Close to 100 different enzymatic modifications of bile acids structures occur in the human intestine and clinically guided metagenomic and metabolomic analyses have led to the identification of an extraordinary number of novel metabolites. These chemical mediators make an essential contribution to the composition and function of the postbiota, participating to the bidirectional communications of the intestinal microbiota with the host and contributing to the architecture of intestinal-liver and -brain and -endocrine axes. Bile acids exert their function by binding to a group of cell membrane and nuclear receptors collectively known as bile acid-regulated receptors (BARRs), expressed in monocytes, tissue-resident macrophages, CD4+ T effector cells, including Th17, T regulatory cells, dendritic cells and type 3 of intestinal lymphoid cells and NKT cells, highlighting their role in immune regulation. In this review we report on how bile acids and their metabolitesmodulate the immune system in inflammations and cancers and could be exploiting for developing novel therapeutic approaches in these disorders.},
}

Humans
*Bile Acids and Salts/metabolism/immunology
Animals
Gastrointestinal Microbiome/immunology

@article {pmid39098060,
year = {2024},
author = {Cojkic, A and Niazi, A and Morrell, JM},
title = {Metagenomic identification of bull semen microbiota in different seasons.},
journal = {Animal reproduction science},
volume = {268},
number = {},
pages = {107569},
doi = {10.1016/j.anireprosci.2024.107569},
pmid = {39098060},
issn = {1873-2232},
mesh = {Male ; Animals ; *Seasons ; Cattle ; *Semen/microbiology ; *Microbiota ; *Semen Analysis/veterinary ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Spermatozoa/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {A seasonal effect on sperm quality parameters was observed previously. Although identification of the bull semen microbiota by 16S rRNA sequencing was performed previously, it has not been carried out in commercial semen samples from different seasons, and its connection with sperm quality parameters has not been evaluated yet. The objectives in this study were; (i) to evaluate diversity of bull semen microbiota and sperm quality parameters in different seasons, and (ii) to find if specific bacteria were associated with seasonal differences in specific sperm quality parameters. Bull semen microbiota was identified in 54 commercial bull semen samples from 3 seasons (winter, spring, summer). Sperm quality was analysed by Computer Assisted Sperm Analyses (CASA) and Flow Cytometry (FC). From 28 phyla in all samples, six phyla were identified in samples from all seasons, with observed seasonal differences in their distribution. At genus level, 388 genera were identified, of which 22 genera had a relative abundance over 1 % and showed seasonal differences in bacterial diversity, and 9 bacteria genera were present in all seasons. Differences between spring and summer (P < 0.05) were observed for live hydrogen peroxide positive sperm cells. A trend towards significance (0.10 > P > 0.05) was observed for some CASA kinematics (VCL and LIN) and FC parameters (High respiratory activity, and live hydrogen peroxide positive sperm cells) between seasons. Nevertheless, associations between sperm quality parameters and specific bacteria were observed in spring.},
}

Male
Animals
*Seasons
Cattle
*Semen/microbiology
*Microbiota
*Semen Analysis/veterinary
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Spermatozoa/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid39024692,
year = {2024},
author = {Chen, L and Bao, Y and Wang, D and Tian, Y and Zeng, T and Gu, T and Xu, W and Lu, L},
title = {Integrated omics analysis reveals the differentiation of intestinal microbiota and metabolites between Pekin ducks and Shaoxing ducks.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103976},
pmid = {39024692},
issn = {1525-3171},
mesh = {Animals ; *Ducks ; *Gastrointestinal Microbiome ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {Pekin ducks and Shaoxing ducks are 2 Chinese local duck breeds, both domesticated from mallard, but after domestication and long-term artificial selection, the body weight of Pekin ducks is significantly higher than that of Shaoxing ducks. It is no debate that genetic factors are the main factors responsible for this difference, but whether intestinal microbiota contribute to this difference is yet unknown. Thus, we performed comparative intestinal metagenomics and metabolomics analysis between Pekin ducks and Shaoxing ducks. We found obvious differentiation of intestinal metagenome and metabolome between the 2 breeds. Four cecal microbial genera, including Fusobacterium, Methanobrevibacter, Butyricicoccus, and Anaerotignum showed higher abundance in Pekin ducks. Among them, Methanobrevibacter and Butyricicoccus may positively correlate with fat deposition and body weight. A total of 310 metabolites showed difference between the 2 breeds. Functions of these differential metabolites were mainly enriched in amino acid metabolism, including energy metabolism-related histidine metabolism. Integrated omics analysis showed that microbial changes were closely related to altered metabolites. Especially, Butyricicoccus showing higher abundance in Pekin ducks was significantly negatively correlated with D-glucosamine-6-phosphate, which has been reported to prevent body weight gains. These findings may contribute to further understand the difference in body weight between Pekin ducks and Shaoxing ducks.},
}

Animals
*Ducks
*Gastrointestinal Microbiome
Metabolome
Metabolomics
Metagenome
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid38945001,
year = {2024},
author = {Schäfer, L and Grundmann, SM and Rühl, M and Zorn, H and Seel, W and Simon, MC and Schuchardt, S and Most, E and Ringseis, R and Eder, K},
title = {Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103975},
pmid = {38945001},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Pleurotus ; *Animal Feed/analysis ; Male ; *Transcriptome ; *Liver/metabolism ; *Diet/veterinary ; *Metabolome ; *Mycelium ; *Dietary Supplements/analysis ; Random Allocation ; },
abstract = {Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 males, 1-day-old Cobb 500 broilers were randomly assigned to 3 different groups and fed 3 different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a 3-phase feeding system for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of 2 low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.},
}

Animals
*Chickens
*Gastrointestinal Microbiome
*Pleurotus
*Animal Feed/analysis
Male
*Transcriptome
*Liver/metabolism
*Diet/veterinary
*Metabolome
*Mycelium
*Dietary Supplements/analysis
Random Allocation

@article {pmid38755047,
year = {2024},
author = {Wang, Y and Yao, J and Zhu, Y and Yin, Z and Zhao, X},
title = {Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {25},
number = {3},
pages = {239-249},
doi = {10.1016/j.ajg.2023.12.009},
pmid = {38755047},
issn = {2090-2387},
mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Dyspepsia/drug therapy/metabolism/microbiology ; *Disease Models, Animal ; Male ; Duodenum/metabolism/microbiology ; Intestinal Mucosa/metabolism/drug effects ; Colon/metabolism ; Drug Therapy, Combination ; },
abstract = {BACKGROUND AND STUDY AIMS: The integration of traditional Chinese medicine and Western medicine holds promise for the treatment of gastrointestinal disorders, which are influenced by intestinal microbiota and metabolites. This study reports a possible mechanism for the combination of Simo Decoction and Golden Bifid in functional dyspepsia (FD) by regulating intestinal microbiota and short-chain fatty acids (SCFAs).

PATIENTS AND METHODS: A mouse model of food stagnation was constructed and treated with Simo Decoction combined with different concentrations of Golden Bifid. Meta-genomics sequencing was conducted to analyze the cecum contents of the mice. Following analyses of the composition and abundance of intestinal microbiota, gas chromatography-mass spectrometry was performed to measure SCFAs in the colonic content of mice. Finally, ELISA was utilized to determine the levels of pro-inflammatory factors in the duodenal mucosa of mice and the infiltration of eosinophils in the duodenum was observed by immunohistochemical staining.

RESULTS: Combination of Simo Decoction and Golden Bifid more significantly alleviated dyspepsia in mice with food stagnation compared with Simo Decoction alone. The optimal ratio of combined treatment was 0.0075 mL/g (body weight) Simo Decoction and 0.0032 mg/g (body weight) Golden Bifid. The combined treatment increased the abundance of Bifidobacterium and Bacteroides in the intestine. The levels of SCFAs in the colonic contents of mice were increased after the combined treatment, contributing to diminished pro-inflammatory factors in the duodenal mucosa and reduced eosinophil infiltration.

CONCLUSION: Combination of Simo Decoction and Golden Bifid increases the abundance of Bacteroides and Bifidobacterium and promotes the production of SCFAs, which is instrumental for alleviation of FD.},
}

Animals
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology
*Dyspepsia/drug therapy/metabolism/microbiology
*Disease Models, Animal
Male
Duodenum/metabolism/microbiology
Intestinal Mucosa/metabolism/drug effects
Colon/metabolism
Drug Therapy, Combination

@article {pmid39180123,
year = {2024},
author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE},
title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {195},
pmid = {39180123},
issn = {1743-422X},
support = {1R01A|129822-01/NH/NIH HHS/United States ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation & purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; },
abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.},
}