@article {pmid40025414,
year = {2025},
author = {Izhar, MZ and Nawaz, M and Yaqub, T and Avais, M},
title = {Effect of probiotic Lactobacillus plantarum CM49 on microbial profile and lactobacilli counts in milk of mastitic cattle.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {109},
pmid = {40025414},
issn = {1471-2180},
support = {PHEC/ARA/PIRCA/20211/9//Punjab Higher Education Commission, Pakistan/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Cattle ; *Milk/microbiology ; Female ; *Lactobacillus plantarum/isolation & purification/genetics ; *Mastitis, Bovine/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Load ; DNA, Bacterial/genetics ; Microbiota/drug effects ; Lactobacillus/isolation & purification/genetics/classification ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification/drug effects ; Streptococcus/genetics/isolation & purification/drug effects ; },
abstract = {BACKGROUND: Bovine mastitis is a common udder disease in cattle, mainly caused by bacteria and other infectious agents. Traditionally antibiotics are used for their treatment, but the development of antibiotic resistance has increased the importance of using non antibiotic alternative such as probiotic. In current study a previously in vitro characterized isolate Lactobacillus plantarum CM49 infused into two groups of cattle suffering from clinical mastitis (n = 5) and sub-clinical mastitis (n = 5).

RESULTS: The bacterial composition and diversity analysis of milk samples before and after probiotic administration was analyzed using 16S rRNA gene base metagenomic analysis and lactobacillus counts were also evaluated using Real time PCR. The results show that there was an increase in abundance of Proteobacteria and decrease in Firmicutes at phylum level in both groups while major mastitogens genera Staphylococcus and Streptococcus abundance was reduced after treatment in sub-clinical mastitis group (SCMG) and clinical mastitis group (CMG) respectively. Lactobacilli counts evaluated through Real time PCR showed an increase in number, furthermore diversity indices showed an increase in diversity after treatment with probiotic.

CONCLUSION: It is concluded from the results that Lactobacillus plantarum CM49 may serve as promising candidate for improving dysbiosis resulting from mastitis and improving microbial diversity.},
}

Animals
*Probiotics/administration & dosage/pharmacology
Cattle
*Milk/microbiology
Female
*Lactobacillus plantarum/isolation & purification/genetics
*Mastitis, Bovine/microbiology
*RNA, Ribosomal, 16S/genetics
Bacterial Load
DNA, Bacterial/genetics
Microbiota/drug effects
Lactobacillus/isolation & purification/genetics/classification
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification/drug effects
Streptococcus/genetics/isolation & purification/drug effects

@article {pmid40025399,
year = {2025},
author = {Liu, A and Wu, J and Li, J and Li, Q and Zhao, N and Hu, K and Liu, S and Blaiotta, G and Zhou, J},
title = {Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {3},
pages = {91},
pmid = {40025399},
issn = {1573-0972},
support = {No. 2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; },
mesh = {*Acetic Acid/metabolism ; *Metagenomics ; *Fermentation ; China ; *Metabolic Networks and Pathways ; *Lactic Acid/metabolism ; *Microbiota ; Acetobacter/metabolism/genetics ; Bacteria/genetics/metabolism/classification ; Lactobacillus/metabolism/genetics ; Food Microbiology ; Phylogeny ; },
abstract = {Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.},
}

*Acetic Acid/metabolism
*Metagenomics
*Fermentation
China
*Metabolic Networks and Pathways
*Lactic Acid/metabolism
*Microbiota
Acetobacter/metabolism/genetics
Bacteria/genetics/metabolism/classification
Lactobacillus/metabolism/genetics
Food Microbiology
Phylogeny

@article {pmid40025082,
year = {2025},
author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G},
title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {367},
pmid = {40025082},
issn = {2052-4463},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Metagenome ; Metagenomics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Archaea/genetics ; South Australia ; },
abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.},
}

*Triticum/microbiology
*Rhizosphere
*Microbiota
*Soil Microbiology
Metagenome
Metagenomics
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing
Archaea/genetics
South Australia

@article {pmid40023383,
year = {2025},
author = {Zhang, Y and Zhang, H and Zhang, B},
title = {Biological and terrestrial influences on dissolved organic matter in Antarctic surface waters: insights from mass spectrometry and metagenomic analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121252},
doi = {10.1016/j.envres.2025.121252},
pmid = {40023383},
issn = {1096-0953},
abstract = {Global warming increases the surface waters and biodiversity in polar regions. However, the intrinsic biological sources of dissolved organic matter (DOM) in Antarctic surface waters remain poorly understood. This work evaluated the sources and driving mechanisms of DOM in Antarctic lakes systematically, based on fluorescence excitation-emission matrices, ultrahigh-resolution mass spectra, biological detection, and metagenomic analyses. The most abundant DOM in the water was peptides (37.02%), which differed from those in soil (lignins: 26.33%) and penguin guano (lipids: 50.71%). The relative abundance of CHON and CHOP compounds in water was significantly correlated with the distance from the penguin colony (p < 0.05). Both the fluorescence and mass spectrum fingerprints of water and soil/faeces showed low similarities using end-member source tracking methods. This could be attributed to the facilitation of guano-derived nutrients and organic carbon to phytoplankton proliferation, whereas the concentrations of NH4[+]-N, NO3[-]-N, total phosphorus, and total organic carbon were significantly higher in the penguin-intensive area than in the other areas. Algae had significant positive effects on carbohydrates and amino sugars and positive effects on lignins, compared to zooplankton and bacteria. Zooplankton had significantly more positive effects on peptides than phytoplankton. Secondary bacterial metabolic activity can be positively linked with CHO compounds. Carbohydrates and amino sugars co-occurred with carbohydrate-active enzyme genes and nitrogen cycling genes in one module of the co-occurrence network, whereas the other module was characterised by the co-occurrence patterns of condensed aromatic structures with carbohydrate-active enzyme genes and nitrogen cycling genes. These results emphasise the roles of secondary metabolites from algae and bacteria in species-specific sources of DOM, shedding light on the driving mechanisms of the biogeochemical cycling of DOM in the Antarctic water environment.},
}

@article {pmid40022370,
year = {2025},
author = {Li, X and You, Y and Xue, B and Chen, J and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J},
title = {Decoding microbiota and metabolite transformation in inoculated fermented suansun using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics:Impacts of different Lactobacillus plantarum strains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115847},
doi = {10.1016/j.foodres.2025.115847},
pmid = {40022370},
issn = {1873-7145},
mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Metabolomics/methods ; *Fermentation ; *Gas Chromatography-Mass Spectrometry ; *Metagenomics/methods ; *Microbiota/physiology/genetics ; Flavoring Agents/metabolism ; Transcriptome ; Gene Expression Profiling ; Fermented Foods/microbiology ; Food Microbiology ; },
abstract = {Using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics, we investigated the microbial communities and metabolites in two different Lactobacillus plantarum fermentations. Metagenomics revealed Weissella cibaria dominantly contributed to the DACN766-fermented suansun (LPS1) and Lactiplantibacillus pentosus to the DACN760-fermented suansun (LPS2). GC-MS identified 38 and 40 flavor compounds in LPS1 and LPS2, respectively, with p-cresol, 4-hydroxybenzaldehyde, acetic acid, hexanal, and propionic acid crucial for aroma development. LPS2 exhibited higher levels of p-cresol and acetic acid, contributing to its stronger sour and pungent flavors, which was achieved by regulating many metabolisms like glycolysis and tyrosine metabolism. In contrast, Weissella cibaria plays a role in mitigating off-flavors, resulting in a milder flavor profile in LPS1. Non-targeted metabolomics indicated 70.78% of differential metabolites were upregulated in LPS1. Conversely, the elevated expression of tryptophan and tyrosine underscores the more pronounced sour and odor-producing characteristics observed in LPS2. Metatranscriptomics highlighted the regulation of genes like XFA, XFT, and XFM, which inhibit the formation of the precursors of p-cresol and indole in LPS2. This integrated multi-omics analysis provides deep insights into the fermentation dynamics, facilitating the targeted selection of Lactobacillus plantarum strains with flavor-regulating capabilities.},
}

*Lactobacillus plantarum/metabolism/genetics
*Metabolomics/methods
*Fermentation
*Gas Chromatography-Mass Spectrometry
*Metagenomics/methods
*Microbiota/physiology/genetics
Flavoring Agents/metabolism
Transcriptome
Gene Expression Profiling
Fermented Foods/microbiology
Food Microbiology

@article {pmid39978123,
year = {2025},
author = {Jin, G and Wang, X and Cui, R and Yuan, S and Wang, M and Chen, Z},
title = {Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes.},
journal = {Water research},
volume = {276},
number = {},
pages = {123262},
doi = {10.1016/j.watres.2025.123262},
pmid = {39978123},
issn = {1879-2448},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics ; Trimethoprim/pharmacology ; Risk Assessment ; Water Pollutants, Chemical ; Lincomycin/pharmacology ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Bacteria/drug effects/genetics
Trimethoprim/pharmacology
Risk Assessment
Water Pollutants, Chemical
Lincomycin/pharmacology
Water Microbiology
Drug Resistance, Bacterial/genetics

@article {pmid39954460,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Ren, J and Qi, J and Zhu, M and Feng, Y and Li, M and Wang, B and Li, X and Song, C},
title = {Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.},
journal = {Water research},
volume = {276},
number = {},
pages = {123285},
doi = {10.1016/j.watres.2025.123285},
pmid = {39954460},
issn = {1879-2448},
mesh = {*Wetlands ; *Phosphorus/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Salinity ; China ; *Soil Microbiology ; Microbiota ; Soil/chemistry ; },
abstract = {Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.},
}

*Wetlands
*Phosphorus/metabolism
*Nitrogen/metabolism
*Carbon/metabolism
*Salinity
China
*Soil Microbiology
Microbiota
Soil/chemistry

@article {pmid39953749,
year = {2025},
author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A},
title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.},
journal = {Molecular ecology},
volume = {34},
number = {6},
pages = {e17695},
doi = {10.1111/mec.17695},
pmid = {39953749},
issn = {1365-294X},
support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Cats ; Metagenomics ; Animals, Wild/microbiology ; Male ; Female ; Metagenome ; },
abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.},
}

Animals
*Gastrointestinal Microbiome/genetics
Cats
Metagenomics
Animals, Wild/microbiology
Male
Female
Metagenome

@article {pmid39931947,
year = {2025},
author = {Liu, Y and Zhao, T and Wang, Z and Zhang, Y and Shen, J and Lu, B},
title = {The microbiome- and metabolome-modulating activity of dietary cholesterol: insights from the small and large intestines.},
journal = {Food & function},
volume = {16},
number = {5},
pages = {1872-1887},
doi = {10.1039/d4fo03049d},
pmid = {39931947},
issn = {2042-650X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Metabolome ; Humans ; *Cholesterol, Dietary/metabolism ; Mice ; Male ; Intestine, Small/metabolism/microbiology ; Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; Bacteria/classification/metabolism/genetics ; },
abstract = {Cholesterol is an important lipid molecule that affects the gut microbiome upon ingestion. We systematically investigated the effects of cholesterol on the microbiota of the large and small intestines using ex vivo and in vivo models, combining flow cytometry, metabolomics, and metagenomics. The results showed that cholesterol directly causes a loss of bacterial membrane polarity and integrity, as well as a reduction in microbial metabolic activity. Cholesterol directly affected the global metabolism of the large and small intestinal microbiota, including amino acid, carbohydrate, and nucleotide metabolism. Ex vivo and in vivo studies shared similar results, showing that cholesterol increased the abundance of the primary bile acid-metabolizing bacteria Clostridium and Dorea in the large intestinal microbiota, confirming the enrichment effect of cholesterol on these bacteria. In the in vivo model, increased conjugated bile acids in the small intestine and decreased abundance of BSH-containing Bifidobacterium were observed due to cholesterol. Only in vivo models have demonstrated that cholesterol increases phosphatidylcholine levels in both the small and large intestines, which may be related to the effects of cholesterol on host metabolism. The pro-inflammatory capacity of the intestinal microbiota was enhanced by cholesterol, as evidenced by the increased levels of IL-1β and TNF-α in THP-1 cells upon stimulation with cholesterol-treated microbiota. This study comprehensively elucidates the effects of cholesterol on the composition and metabolic functions of the microbiota in both the large and small intestines. It offers a novel perspective on the ways in which cholesterol affects host metabolism via the gut microbiome.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Metabolome
Humans
*Cholesterol, Dietary/metabolism
Mice
Male
Intestine, Small/metabolism/microbiology
Bile Acids and Salts/metabolism
Mice, Inbred C57BL
Bacteria/classification/metabolism/genetics

@article {pmid39929376,
year = {2025},
author = {Wu, B and Tang, Y and Zhao, L and Gao, Y and Shen, X and Xiao, S and Yao, S and Qi, H and Shen, F},
title = {Integrated network pharmacological analysis and multi-omics techniques to reveal the mechanism of polydatin in the treatment of silicosis via gut-lung axis.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {207},
number = {},
pages = {107030},
doi = {10.1016/j.ejps.2025.107030},
pmid = {39929376},
issn = {1879-0720},
mesh = {Animals ; *Glucosides/pharmacology/therapeutic use ; *Stilbenes/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Male ; *Lung/drug effects/metabolism ; *Network Pharmacology ; *Molecular Docking Simulation ; *Silicosis/drug therapy/metabolism ; Rats ; Metabolomics/methods ; Rats, Sprague-Dawley ; Multiomics ; },
abstract = {Silicosis is a pulmonary disease characterized by inflammation and progressive fibrosis. Previous studies have shown that polydatin (PD) has potential biological activity in key signaling pathways regulating inflammation and apoptosis. To investigate the effect of PD on rats with silicosis, this study used network pharmacology and molecular docking methods to determine the target of PD treatment for silicosis. The therapeutic effect of PD on silicosis was confirmed by measuring the lung injury score, hydroxyproline content, and mRNA expression levels of key targets. In addition, metagenomic sequencing and gas chromatography-mass spectrometry were used to determine the gut microbiota composition and targeted metabolomics analysis, respectively. The results showed that PD could inhibit the expression of inflammation-related indexes and apoptosis-related indexes at protein and mRNA levels. PD also regulates the diversity of the intestinal flora and the content of short-chain fatty acids. In conclusion, the current data suggest that PD has a protective effect against silica-induced lung injury and plays a protective role in regulating intestinal flora diversity and short-chain fatty acid levels through the gut-lung axis.},
}

Animals
*Glucosides/pharmacology/therapeutic use
*Stilbenes/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Male
*Lung/drug effects/metabolism
*Network Pharmacology
*Molecular Docking Simulation
*Silicosis/drug therapy/metabolism
Rats
Metabolomics/methods
Rats, Sprague-Dawley
Multiomics

@article {pmid39917835,
year = {2025},
author = {Hoffbeck, C and Middleton, DMRL and Wallbank, JA and Boey, JS and Taylor, MW},
title = {Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts.},
journal = {Molecular ecology},
volume = {34},
number = {6},
pages = {e17685},
doi = {10.1111/mec.17685},
pmid = {39917835},
issn = {1365-294X},
support = {//University of Auckland Doctoral Scholarship/ ; },
mesh = {Animals ; *Reptiles/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteroides/genetics/classification ; *Metagenome/genetics ; Phylogeny ; },
abstract = {The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.},
}

Animals
*Reptiles/microbiology
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Bacteroides/genetics/classification
*Metagenome/genetics
Phylogeny

@article {pmid39855018,
year = {2025},
author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Zhu, X and Yin, H and Dang, Z and Niu, J},
title = {Metagenomic and enzymatic mechanisms underpinning efficient water treatment of 2-ethylhexyl diphenyl phosphate (EHDPP) by the microbial consortium 8-ZY.},
journal = {Water research},
volume = {275},
number = {},
pages = {123178},
doi = {10.1016/j.watres.2025.123178},
pmid = {39855018},
issn = {1879-2448},
mesh = {*Microbial Consortia ; *Water Purification ; Biodegradation, Environmental ; Metagenomics ; Water Pollutants, Chemical/metabolism ; },
abstract = {The ubiquitous presence, potential toxicity, and persistence of 2-ethylhexyl diphenyl phosphate (EHDPP) in the environment have raised significant concerns. In this study, we successfully isolate a novel microbial consortium, named 8-ZY, and we demonstrate its remarkable ability to degrade EHDPP using an extremely low concentration of the inoculate. A total of 11 degradation metabolites were identified, including hydrolysis, hydroxylated, methylated, glucuronide-conjugated, and previously unreported byproducts, enabling us to propose new transformation pathways. Further, we unveiled the active members of the microbial consortium 8-ZY during the degradation of EHDPP. We observed the presence of diverse active populations, which included Bradyrhizobium, Rhodopseudomonas, Sphingomonas, Hyphomicrobium, Chitinophaga, Aminobacter, and Ralstonia. A metagenomic analysis revealed the presence of genes that encode phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase enzymes, thus indicating their crucial role in EHDPP degradation. Furthermore, we successfully isolated Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 from the 8-ZY consortium, confirming their significance in EHDPP degradation and metabolite formation. These findings underscored the diversity of strains and functional genes responsible for the transformation of EHDPP within the consortium 8-ZY, highlighting the essential role of synergistic interactions during EHDPP biodegradation processes. Molecular docking and dynamics simulation suggested that alkaline phosphatase, cytochrome P450, and hydroxylase stably bonded to EHDPP within their respective active pockets, targeting distinct sites on the EHDPP molecule. These findings provide a comprehensive understanding of the transformation mechanisms of OPEs and contribute valuable insights into their fate in the environment.},
}

*Microbial Consortia
*Water Purification
Biodegradation, Environmental
Metagenomics
Water Pollutants, Chemical/metabolism

@article {pmid39204265,
year = {2024},
author = {Ariyadasa, S and van Hamelsveld, S and Taylor, W and Lin, S and Sitthirit, P and Pang, L and Billington, C and Weaver, L},
title = {Diversity of Free-Living Amoebae in New Zealand Groundwater and Their Ability to Feed on Legionella pneumophila.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39204265},
issn = {2076-0817},
support = {ESR2023SA1//Ministry of Business, Innovation, and Employment New Zealand/ ; },
mesh = {New Zealand ; *Legionella pneumophila/isolation & purification/genetics ; *Groundwater/microbiology/parasitology ; *Amoeba/microbiology ; Humans ; Biodiversity ; Water Microbiology ; Acanthamoeba/microbiology/isolation & purification/genetics ; Ecosystem ; },
abstract = {Free-living amoebae (FLA) are common in both natural and engineered freshwater ecosystems. They play important roles in biofilm control and contaminant removal through the predation of bacteria and other taxa. Bacterial predation by FLA is also thought to contribute to pathogen dispersal and infectious disease transmission in freshwater environments via the egestion of viable bacteria. Despite their importance in shaping freshwater microbial communities, the diversity and function of FLA in many freshwater ecosystems are poorly understood. In this study, we isolated and characterized FLA from two groundwater sites in Canterbury, New Zealand using microbiological, microscopic, and molecular techniques. Different methods for groundwater FLA isolation and enrichment were trialed and optimized. The ability of these isolated FLA to predate on human pathogen Legionella pneumophila was assessed. FLA were identified by 18S metagenomic amplicon sequencing. Our study showed that Acanthamoeba spp. (including A. polyphaga) and Vermamoeba veriformis were the main FLA species present in both groundwater sites examined. While most of the isolated FLA co-existed with L. pneumophila, the FLA populations in the L. pneumophila co-culture experiments predominantly consisted of A. polyphaga, Acanthamoeba spp., Naegleria spp., V. vermiformis, Paravahlkampfia spp., and Echinamoeba spp. These observations suggest that FLA may have the potential to act as reservoirs for L. pneumophila in Canterbury, New Zealand groundwater systems and could be introduced into the local drinking water infrastructure, where they may promote the survival, multiplication, and dissemination of Legionella. This research addresses an important gap in our understanding of FLA-mediated pathogen dispersal in freshwater ecosystems.},
}

New Zealand
*Legionella pneumophila/isolation & purification/genetics
*Groundwater/microbiology/parasitology
*Amoeba/microbiology
Humans
Biodiversity
Water Microbiology
Acanthamoeba/microbiology/isolation & purification/genetics
Ecosystem

@article {pmid38787271,
year = {2024},
author = {Lundtorp-Olsen, C and Markvart, M and Twetman, S and Belstrøm, D},
title = {Effect of Probiotic Supplements on the Oral Microbiota-A Narrative Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38787271},
issn = {2076-0817},
mesh = {*Probiotics/administration & dosage/pharmacology/therapeutic use ; Humans ; *Microbiota/drug effects ; *Mouth/microbiology ; *Dietary Supplements ; Randomized Controlled Trials as Topic ; Dental Caries/microbiology/prevention & control ; Gingivitis/microbiology/prevention & control ; Periodontitis/microbiology ; },
abstract = {Data from systematic reviews and meta-analyses show that probiotics positively impact clinical parameters of oral diseases such as gingivitis, dental caries, and periodontitis. However, the working mechanism of probiotics is not fully understood, but is hypothesized to be mediated by direct and indirect interactions with the oral microbiota and the human host. In the present narrative review, we focused on the microbiological effect of probiotic supplements based on data retrieved from randomized clinical trials (RCTs). In addition, we assessed to what extent contemporary molecular methods have been employed in clinical trials in the field of oral probiotics. Multiple RCTs have been performed studying the potential effect of probiotics on gingivitis, dental caries, and periodontitis, as evaluated by microbial endpoints. In general, results are conflicting, with some studies reporting a positive effect, whereas others are not able to record any effect. Major differences in terms of study designs and sample size, as well as delivery route, frequency, and duration of probiotic consumption, hamper comparison across studies. In addition, most RCTs have been performed with a limited sample size using relatively simple methods for microbial identification, such as culturing, qPCR, and DNA-DNA checkerboard, while high-throughput methods such as 16S sequencing have only been employed in a few studies. Currently, state-of-the-art molecular methods such as metagenomics, metatranscriptomics, and metaproteomics have not yet been used in RCTs in the field of probiotics. The present narrative review revealed that the effect of probiotic supplements on the oral microbiota remains largely uncovered. One important reason is that most RCTs are performed without studying the microbiological effect. To facilitate future systematic reviews and meta-analyses, an internationally agreed core outcome set for the reporting of microbial endpoints in clinical trials would be desirable. Such a standardized collection of outcomes would most likely improve the quality of probiotic research in the oral context.},
}

*Probiotics/administration & dosage/pharmacology/therapeutic use
Humans
*Microbiota/drug effects
*Mouth/microbiology
*Dietary Supplements
Randomized Controlled Trials as Topic
Dental Caries/microbiology/prevention & control
Gingivitis/microbiology/prevention & control
Periodontitis/microbiology

@article {pmid38392888,
year = {2024},
author = {Ford, CE and Dunn, CD and Leis, EM and Thiel, WA and Goldberg, TL},
title = {Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38392888},
issn = {2076-0817},
support = {R/SFA-24//University of Wisconsin Sea Grant Institute/ ; },
mesh = {Animals ; Wisconsin ; *Fishes/virology ; *Virome/genetics ; *Fresh Water/virology ; Phylogeny ; Fish Diseases/virology/epidemiology ; Viruses/genetics/isolation & purification/classification ; },
abstract = {Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.},
}

Animals
Wisconsin
*Fishes/virology
*Virome/genetics
*Fresh Water/virology
Phylogeny
Fish Diseases/virology/epidemiology
Viruses/genetics/isolation & purification/classification

@article {pmid38392845,
year = {2024},
author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Levy, A and Smith, D and Imrie, A},
title = {Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38392845},
issn = {2076-0817},
mesh = {Animals ; Western Australia ; *RNA Viruses/genetics/isolation & purification ; Microbiota/genetics ; Virome/genetics ; Mosquito Vectors/microbiology/virology ; Culicidae/virology/microbiology ; Aedes/microbiology/virology ; Biodiversity ; Culex/virology/microbiology ; Transcriptome ; Metagenomics/methods ; Phylogeny ; },
abstract = {Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.},
}

Animals
Western Australia
*RNA Viruses/genetics/isolation & purification
Microbiota/genetics
Virome/genetics
Mosquito Vectors/microbiology/virology
Culicidae/virology/microbiology
Aedes/microbiology/virology
Biodiversity
Culex/virology/microbiology
Transcriptome
Metagenomics/methods
Phylogeny

@article {pmid40022356,
year = {2025},
author = {Li, Y and Wu, Y and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wang, Y},
title = {Decoding the aroma landscape of fermented golden pompano: The interplay of ester compounds and symbiotic microbiota as revealed by metagenomics and two-dimensional flavoromics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115832},
doi = {10.1016/j.foodres.2025.115832},
pmid = {40022356},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Esters/metabolism/analysis ; *Microbiota ; Odorants/analysis ; Taste ; Seafood/microbiology ; Flavoring Agents/metabolism ; Animals ; Fermented Foods/microbiology ; Symbiosis ; },
abstract = {Fermented pompano (Trachinotus ovatus) is a traditionally popular fermented seafood throughout Asia. Its distinctive flavor profile is primarily attributed to the microbial metabolic conversion of nutrients, which produces specific volatile compounds. Two-dimensional flavoromics of mature pompano revealed that various volatile flavor compounds accumulate throughout fermentation, with fruity (predominantly esters) and oleogustus (primarily ketones) being key flavor markers. S-curve analysis further demonstrated synergistic and additive interactions between these compounds, which enhance flavor release. Metagenomics and Kyoto Encyclopedia of Genes and Genome analysis revealed that amino acid metabolism was the pivotal pathway for ethyl ester synthesis, with Staphylococcus equorum being positively correlated with esters such as ethyl isobutyrate and ethyl enanthate. This study elucidated the interrelationship between flavor compounds and the microbial community in fermented pompano, which is expected to provide insights into flavor modulation and guide the selection of strains that produce key esters in fermented seafood products.},
}

*Metagenomics/methods
*Fermentation
*Volatile Organic Compounds/analysis/metabolism
*Esters/metabolism/analysis
*Microbiota
Odorants/analysis
Taste
Seafood/microbiology
Flavoring Agents/metabolism
Animals
Fermented Foods/microbiology
Symbiosis

@article {pmid40022320,
year = {2025},
author = {Cámara-Martos, F and Bolívar, A and Rabasco-Vílchez, L and Lafont-Déniz, F and Luque-Ojeda, JL and Pérez-Rodríguez, F},
title = {Exploring the bioaccessibility, in vitro colonic fermentation, and the impact on the intestinal microbiota of allyl-and benzyl-isothiocyanate from white and Ethiopian mustard.},
journal = {Food research international (Ottawa, Ont.)},
volume = {203},
number = {},
pages = {115781},
doi = {10.1016/j.foodres.2025.115781},
pmid = {40022320},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome ; *Mustard Plant/microbiology/chemistry ; *Colon/microbiology/metabolism ; *Fermentation ; *Isothiocyanates/metabolism ; Humans ; Biological Availability ; Digestion ; Glucosinolates/metabolism/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {The aim of this research was to study the formation and bioaccessibility of allyl- and benzyl-isothiocyanate (ITC) resulting from the gastrointestinal digestion (small and large intestine) of green parts from Ethiopian and white mustard. In addition, a GC-MS methodology was validated to determine these compounds in bioaccessible and non-bioaccessible fraction. Plant clumps were divided into two batches: fresh and freeze-dried samples. ITC bioaccessibility was low in the small intestine, with values ranged between 11 and 53 % and mean values of 26 %. These results are in agreement with the fact that ITCs are poorly water-soluble compounds. Bioaccessibility values for lyophilised samples were lower than those obtained in fresh samples. This could be due to the degradation of the precursor glucosinolates (sinigrin and glucotropaeolin respectively). The simulation of the colonic fermentation reduced allyl - and benzyl - ITC levels from the non-bioaccessible fraction of Ethiopian and white mustard (values between 0.009 and 0.087 mg/g). In both cases, ITCs concentration dropped dramatically, i.e. with a ten-fold reduction. Nevertheless, this result does not necessarily indicate that ITCs have not been produced in the large intestine. Bacterial microbiota plays a key role in generating ITCs; however, ITCs are not always the final products of this process. The metagenomic analysis of colonic samples revealed that ITCs and cruciferous matrix significantly influenced the composition of gut microbiota, inhibiting potentially pathogenic bacteria such as Enterobacter and Klebsiella, while promoting beneficial bacteria such as Bifidobacterium, Faecalibacterium, Blautia, and Ruminococcus. Interestingly, ITCs-rich environments selected bacterial species (i.e. Enterobacter ludwigii) and promoted metabolic pathways involved in glucosinolate/ITCs metabolism.},
}

*Gastrointestinal Microbiome
*Mustard Plant/microbiology/chemistry
*Colon/microbiology/metabolism
*Fermentation
*Isothiocyanates/metabolism
Humans
Biological Availability
Digestion
Glucosinolates/metabolism/analysis
Gas Chromatography-Mass Spectrometry

@article {pmid40022097,
year = {2025},
author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ},
title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.},
journal = {BMC urology},
volume = {25},
number = {1},
pages = {41},
pmid = {40022097},
issn = {1471-2490},
mesh = {Humans ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Nanopore Sequencing/methods ; Vagina/microbiology ; Workflow ; Urogenital System/microbiology ; },
abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.},
}

Humans
Female
Male
*Metagenomics/methods
*Microbiota/genetics
Nanopore Sequencing/methods
Vagina/microbiology
Workflow
Urogenital System/microbiology

@article {pmid40022204,
year = {2025},
author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J},
title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {59},
pmid = {40022204},
issn = {2049-2618},
support = {R01AG071684/NH/NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R61AG078470//National Science Foundation/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Papio/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.

RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.

CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.},
}

Animals
*Metagenomics/methods
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation
Humans
Papio/microbiology
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid40021694,
year = {2025},
author = {Gambardella, N and Costa, J and Martins, BM and Folhas, D and Ribeiro, AP and Hintelmann, H and Canário, J and Magalhães, C},
title = {The role of prokaryotic mercury methylators and demethylators in Canadian Arctic thermokarst lakes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7173},
pmid = {40021694},
issn = {2045-2322},
support = {PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Arctic Regions ; Canada ; *Lakes/microbiology ; *Mercury/metabolism ; Methylation ; Methylmercury Compounds/metabolism/analysis ; Microbiota ; Geologic Sediments/microbiology ; Bacteria/genetics/metabolism/classification ; Permafrost/microbiology ; Seasons ; Metagenomics/methods ; Water Pollutants, Chemical/metabolism ; Environmental Monitoring/methods ; },
abstract = {Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation and in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. However, the specific microbes involved still need to be understood. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples from two thermokarst lakes in the Canadian sub-Arctic were collected during the winter and summer of 2022. Gene-centric metagenomics using whole-genome sequencing (WGS) was employed to identify key genes involved in mercury methylation (hgcA and hgcB) and demethylation (merA and merB), supported by qPCR analyses. A seasonal decline in microbial diversity, involved in the Hg methylation, and hgcA gene coverage was observed from winter to summer, mirroring patterns in mercury methylation rates. Notably, hgcA sequences were significantly more abundant than merAB sequences, with contrasting seasonal trends. These results indicate a seasonal shift in the microbial community, transitioning from a dominance of mercury methylation in winter to a predominance of mercury demethylation in summer. Environmental drivers of these dynamics were integrated into a conceptual model. This study provide new insights on the microbial processes influencing the Hg cycle in Arctic permafrost undergoing degradation.},
}

Arctic Regions
Canada
*Lakes/microbiology
*Mercury/metabolism
Methylation
Methylmercury Compounds/metabolism/analysis
Microbiota
Geologic Sediments/microbiology
Bacteria/genetics/metabolism/classification
Permafrost/microbiology
Seasons
Metagenomics/methods
Water Pollutants, Chemical/metabolism
Environmental Monitoring/methods

@article {pmid40020468,
year = {2025},
author = {Huang, Y and Li, XT and Jiang, Z and Liang, ZL and Liu, W and Liu, ZH and Li, LZ and Yang, ZN and Zhang, GQ and Yin, HQ and Liang, JL and Zhou, N and Liu, SJ and Jiang, CY},
title = {Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage.},
journal = {Water research},
volume = {278},
number = {},
pages = {123367},
doi = {10.1016/j.watres.2025.123367},
pmid = {40020468},
issn = {1879-2448},
abstract = {Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.},
}

@article {pmid40020117,
year = {2025},
author = {Zheng, X and Fan, J and Yin, J and Chu, Y},
title = {The role of gut microbiota and plasma metabolites in ulcerative colitis: Insights from Mendelian randomization analysis.},
journal = {Medicine},
volume = {104},
number = {9},
pages = {e41710},
pmid = {40020117},
issn = {1536-5964},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/blood/microbiology ; *Genome-Wide Association Study ; },
abstract = {Emerging research suggests that alterations in gut microbiota composition may play a significant role in the pathogenesis of ulcerative colitis (UC). Plasma metabolites, which are influenced by gut microbiota, have also been implicated, but their role in UC remains unclear. This study aims to determine whether specific plasma metabolites mediate the causal relationship between gut microbiota and UC using Mendelian randomization (MR) analysis. This study employed publicly available summary-level data from genome-wide association studies and metagenomic datasets. Gut microbiota data were derived from the FINRISK cohort (5959 participants), plasma metabolite data from the Canadian Longitudinal Study on Aging (8299 individuals), and UC data from multiple consortia (17,030 cases and 883,787 controls). Forward and reverse MR analyses, supplemented by linkage disequilibrium score regression (LDSC), were conducted to assess causal relationships. Mediation effects of plasma metabolites between gut microbiota and UC were analyzed using the product of coefficients method. Various sensitivity analyses, including MR-Egger and MR-PRESSO, were applied to detect pleiotropy and ensure robust results. The study identified 20 bacterial taxa and 93 plasma metabolites linked to UC. Forward MR analysis showed that Clostridium S felsineum increased UC risk via reduced carnitine levels, with a mediation proportion of 39.77%. Eubacterium callanderi was associated with decreased UC risk through the tryptophan to pyruvate ratio (16.02% mediation). Additionally, species CAG-590 sp000431135 increased UC risk through elevated mannitol/sorbitol levels, mediating 28.38% of the effect. Sensitivity analyses confirmed the robustness of these findings, with minimal heterogeneity and pleiotropy detected. This study highlights the significant role of gut microbiota and their associated plasma metabolites in the pathogenesis of UC. Specific microbial species influence UC through metabolites, suggesting potential therapeutic targets. Modulating carnitine, tryptophan metabolism, or sugar alcohols could offer promising avenues for UC management.},
}

Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome
*Colitis, Ulcerative/blood/microbiology
*Genome-Wide Association Study

@article {pmid40016914,
year = {2025},
author = {Lu, X and Xu, Y and Liu, Y and Li, F and Feng, Q and Gao, C and Liu, D and Zhou, L and Yang, H and Zhang, J and Cui, F and Chen, Q},
title = {Neutrophil Depletion Reduced the Relative Abundance of Unsaturated Long-Chain Fatty Acid Synthesis Microbiota and Intestinal Lipid Absorption.},
journal = {Cell biochemistry and function},
volume = {43},
number = {3},
pages = {e70060},
doi = {10.1002/cbf.70060},
pmid = {40016914},
issn = {1099-0844},
support = {//This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Suzhou Fundamental Research Project (SJC2023001), and Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges. It was funded by the National Natural Science Foundation of China (Grant No. 81773355)./ ; },
mesh = {Animals ; Mice ; *Neutrophils/metabolism ; *Intestinal Absorption ; Male ; Gastrointestinal Microbiome ; Lipid Metabolism ; Mice, Inbred C57BL ; Fatty Acids, Unsaturated/metabolism ; Rats ; },
abstract = {As immune cells, neutrophils serve as the first line of defense against infections; however, the mechanism by which neutrophils regulate lipid metabolism is unknown. The neutrophil depletion group was treated with 100 μg InVivoMAb anti-mouse Ly6G 6 times, whereas the control group mice were intraperitoneally injected with the same quantity of InVivoMAb rat IgG2a. Body fat content, triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) in the jejunum and ileum, as well as 9 long-chain fatty acids (LCFAs) in the intestinal contents were significantly decreased. Furthermore, genes involved in the absorption of lipids in each segment of the intestine also showed decreased expression. Neutrophil-depletion and control models were administered 25 μCi of [3]H-cholesterol by gavage. The distribution of [3]H cholesterol in the intestinal segment, heart, liver, serum, and feces was not altered by anti-Ly6G antibodies. Metagenomics was applied to investigate uncultured microorganisms in the intestinal contents to identify bacteria containing lipid metabolism genes. At the species level, 12 bacteria were involved in unsaturated LCFA synthesis, among which 2 increased and 10 decreased. The overall relative abundance of these bacteria decreased from 3.102% to 0.734%. Many genes involved in lipid metabolism were also reduced as a result, such as fatty acid synthase and peroxisome proliferator-activated receptor γ. In conclusion, neutrophil depletion does not affect intestinal lipid absorption in the diet but leads to a decrease in the overall relative abundance of gut bacteria involved in unsaturated LCFA synthesis. Consequently, intestinal lipid synthesis and absorption are reduced.},
}

Animals
Mice
*Neutrophils/metabolism
*Intestinal Absorption
Male
Gastrointestinal Microbiome
Lipid Metabolism
Mice, Inbred C57BL
Fatty Acids, Unsaturated/metabolism
Rats

@article {pmid39923562,
year = {2025},
author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E},
title = {The microbiome of Total Suspended Particles and its influence on the respiratory microbiome of healthy office workers.},
journal = {Ecotoxicology and environmental safety},
volume = {291},
number = {},
pages = {117874},
doi = {10.1016/j.ecoenv.2025.117874},
pmid = {39923562},
issn = {1090-2414},
mesh = {Humans ; *Microbiota/drug effects ; *Particulate Matter/analysis ; *Air Pollution, Indoor/analysis ; *Air Microbiology ; Air Pollutants/analysis ; Environmental Monitoring ; Occupational Exposure/analysis ; Bacteria/classification/genetics/isolation & purification ; Respiratory System/microbiology ; Italy ; Adult ; },
abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.},
}

Humans
*Microbiota/drug effects
*Particulate Matter/analysis
*Air Pollution, Indoor/analysis
*Air Microbiology
Air Pollutants/analysis
Environmental Monitoring
Occupational Exposure/analysis
Bacteria/classification/genetics/isolation & purification
Respiratory System/microbiology
Italy
Adult

@article {pmid39922085,
year = {2025},
author = {Florio, M and Crudele, L and Sallustio, F and Moschetta, A and Cariello, M and Gadaleta, RM},
title = {Disentangling the nutrition-microbiota liaison in inflammatory bowel disease.},
journal = {Molecular aspects of medicine},
volume = {102},
number = {},
pages = {101349},
doi = {10.1016/j.mam.2025.101349},
pmid = {39922085},
issn = {1872-9452},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/diet therapy ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Nutritional Status ; Animals ; Diet ; },
abstract = {Inflammatory Bowel Disease (IBD) is a set of chronic intestinal inflammatory disorders affecting the gastrointestinal (GI) tract. Beside compromised intestinal barrier function and immune hyperactivation, a common IBD feature is dysbiosis, characterized by a reduction of some strains of Firmicutes, Bacteroidetes, Actinobacteria and an increase in Proteobacteria and pathobionts. Emerging evidence points to diet and nutrition-dependent gut microbiota (GM) modulation, as etiopathogenetic factors and adjuvant therapies in IBD. Currently, no nutritional regimen shows universal efficacy, and advice are controversial, especially those involving restrictive diets potentially resulting in malnutrition. This review provides an overview of the role of macronutrients, dietary protocols and GM modulation in IBD patients. A Western-like diet contributes to an aberrant mucosal immune response to commensal bacteria and impairment of the intestinal barrier integrity, thereby triggering intestinal inflammation. Conversely, a Mediterranean nutritional pattern appears to be one of the most beneficial dietetic regimens able to restore the host intestinal physiology, by promoting eubiosis and preserving the intestinal barrier and immune function, which in turn create a virtuous cycle improving patient adherence to the pattern. Further clinical studies are warranted, to corroborate current IBD nutritional guidelines, and develop more accurate models to move forward precision nutrition and ameliorate patients' quality of life.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/diet therapy
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Nutritional Status
Animals
Diet

@article {pmid39908950,
year = {2025},
author = {Alonso-Vásquez, T and Fagorzi, C and Mengoni, A and Oliva, M and Cavalieri, D and Pretti, C and Cangioli, L and Bacci, G and Ugolini, A},
title = {Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area.},
journal = {Marine pollution bulletin},
volume = {213},
number = {},
pages = {117640},
doi = {10.1016/j.marpolbul.2025.117640},
pmid = {39908950},
issn = {1879-3363},
mesh = {*Geologic Sediments/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Italy ; Metagenomics ; Metagenome ; Microbiota/drug effects ; Urbanization ; },
abstract = {Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.},
}

*Geologic Sediments/microbiology
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects
RNA, Ribosomal, 16S
Environmental Monitoring
Italy
Metagenomics
Metagenome
Microbiota/drug effects
Urbanization

@article {pmid39904008,
year = {2025},
author = {Bohra, V and Lai, KK and Lam, KL and Tam, NF and Jing-Liang, S and Lee, FW},
title = {Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices.},
journal = {Marine pollution bulletin},
volume = {213},
number = {},
pages = {117614},
doi = {10.1016/j.marpolbul.2025.117614},
pmid = {39904008},
issn = {1879-3363},
mesh = {*Metagenomics ; *Wetlands ; *Avicennia/microbiology ; *Microbiota ; *Bacteria/genetics ; *Geologic Sediments/microbiology ; },
abstract = {Present research employed metagenomics to explore the structural and functional diversity of microorganisms in two matrices of pneumatophore: adhered sediments (PS) and epiphytes (PE) of Avicennia marina. These were compared with microorganisms in surrounding environments: tidal water (TW), mudflat sediment (MF) and mangrove sediment (MS). Results revealed that bacteria made up over 95 % of the microbial community across all five matrices, with the dominance of phylum Proteobacteria, because of their metabolic flexibility and ability to survive in harsh mangrove environment. The bacterial community in PS and PE were similar to TW but differed from those in MF and MS, implying their provenance from TW. The high relative abundance of genes involved in nitrate and sulfur reduction pathways in PS and PE indicates pneumatophore bacteria helps in enhancing nitrogen and sulfur availability. This study is the first to explore the functional significance of pneumatophore-adhered prokaryotic communities using metagenomics.},
}

*Metagenomics
*Wetlands
*Avicennia/microbiology
*Microbiota
*Bacteria/genetics
*Geologic Sediments/microbiology

@article {pmid39778631,
year = {2025},
author = {Harriman, D and Ng, A and Bronowski, M and Kazakov, H and Nguan, C and Dang, T and Sherwood, K and Miller, A and Lange, D},
title = {Characterizing the urobiome and associated metabolic profiles during acute rejection in renal transplant patients: A pilot study.},
journal = {Transplant immunology},
volume = {89},
number = {},
pages = {102170},
doi = {10.1016/j.trim.2024.102170},
pmid = {39778631},
issn = {1878-5492},
mesh = {Humans ; *Kidney Transplantation ; *Graft Rejection/diagnosis ; Pilot Projects ; Male ; Female ; Middle Aged ; Adult ; Metabolome ; Acute Disease ; Microbiota ; Aged ; },
abstract = {Characteristic alterations in the urinary microbiome, or urobiome, are associated with renal transplant pathology. To date, there has been no direct study of the urobiome during acute allograft rejection. The goal of this study was to determine if unique urobiome alterations are present during acute rejection in renal transplant recipients. We performed shotgun metagenomic sequencing of 32 mid-stream urine samples obtained from 15 transplant recipients pre-transplant, 1- and 3-months post-transplant, and at time of rejection discovered with for-cause biopsy. Within individuals, there was a 40-60 % difference in urobiome composition from pre-to-post-transplant in both rejectors and non-rejectors. The taxa Ureaplasma was enriched in rejectors compared to non-rejectors. However, a greater number of microbial genes were enriched in non-rejectors compared to rejectors, except for genes associated with tetracycline resistance, the lysophosphatidic acid synthesis pathway, and tryptophanyl-tRNA synthetase. Together, our findings suggest that the urobiome is significantly altered post-transplant with certain taxa and/or microbial genes potentially associated with acute allograft rejection/inflammation.},
}

Humans
*Kidney Transplantation
*Graft Rejection/diagnosis
Pilot Projects
Male
Female
Middle Aged
Adult
Metabolome
Acute Disease
Microbiota
Aged

@article {pmid39622769,
year = {2025},
author = {Ivan, FX and Tiew, PY and Jaggi, TK and Thng, KX and Pang, PH and Ong, TH and Abisheganaden, JA and Koh, MS and Chotirmall, SH},
title = {Sputum metagenomics reveals a multidrug resistant Pseudomonas-dominant severe asthma phenotype in an Asian population.},
journal = {Respirology (Carlton, Vic.)},
volume = {30},
number = {3},
pages = {217-229},
doi = {10.1111/resp.14863},
pmid = {39622769},
issn = {1440-1843},
support = {AcRF Tier 1 Grant (RT1/22)//Singapore Ministry of Education/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001636//Singapore Ministry of Health's National Medical Research Council/ ; },
mesh = {Humans ; *Sputum/microbiology ; *Asthma/microbiology ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Singapore/epidemiology ; *Phenotype ; Prospective Studies ; *Asian People/genetics ; Adult ; Pseudomonas Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbiota/genetics ; Severity of Illness Index ; Pseudomonas aeruginosa/isolation & purification/genetics ; Pseudomonas/genetics/isolation & purification ; Aged ; Bronchiectasis/microbiology ; },
abstract = {BACKGROUND AND OBJECTIVE: While the lung microbiome in severe asthma has been studied, work has employed targeted amplicon-based sequencing approaches without functional assessment with none focused on multi-ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.

METHODS: Prospective assessment of clinical, radiological, and immunological measures were performed in a multi-ethnic Asian severe asthma cohort (N = 70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2-year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.

RESULTS: The lung microbiome in a multi-ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n = 52) characterized by upper airway commensals and C2 (n = 18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2-year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co-existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non-asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.

CONCLUSION: Sputum metagenomics demonstrates a multidrug-resistant Pseudomonas-dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co-existing bronchiectasis.},
}

Humans
*Sputum/microbiology
*Asthma/microbiology
Male
Female
*Metagenomics/methods
Middle Aged
Singapore/epidemiology
*Phenotype
Prospective Studies
*Asian People/genetics
Adult
Pseudomonas Infections/microbiology
Drug Resistance, Multiple, Bacterial/genetics
Microbiota/genetics
Severity of Illness Index
Pseudomonas aeruginosa/isolation & purification/genetics
Pseudomonas/genetics/isolation & purification
Aged
Bronchiectasis/microbiology

@article {pmid38987012,
year = {2025},
author = {Caceres Lessa, AY and Edwinson, A and Sato, H and Yang, L and Berumen, A and Breen-Lyles, M and Byale, A and Ryks, M and Keehn, A and Camilleri, M and Farrugia, G and Chen, J and Decuir, M and Smith, K and Dasari, S and Grover, M},
title = {Transcriptomic and Metabolomic Correlates of Increased Colonic Permeability in Postinfection Irritable Bowel Syndrome.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {23},
number = {4},
pages = {632-643.e13},
pmid = {38987012},
issn = {1542-7714},
support = {K23 DK103911/DK/NIDDK NIH HHS/United States ; R01 DK127998/DK/NIDDK NIH HHS/United States ; R03 DK120745/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/metabolism/genetics/microbiology ; Female ; Male ; Middle Aged ; Adult ; *Permeability ; *Feces/chemistry/microbiology ; *Colon/metabolism/microbiology ; Gastrointestinal Microbiome/physiology ; Transcriptome ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND & AIMS: Postinfection irritable bowel syndrome (PI-IBS) is well-known epidemiologically; however, its physiological and molecular characteristics are not well studied. We aimed to determine the physiological phenotypes, colonic transcriptome, fecal microbiome, and metabolome in PI-IBS.

METHODS: Fifty-one Rome III Campylobacter PI-IBS patients and 39 healthy volunteers (HV) were enrolled. Participants completed questionnaires, in vivo intestinal permeability, gastrointestinal transit, and rectal sensation. Fecal samples were collected for shotgun metagenomics, untargeted metabolomics, and sigmoid colonic biopsies for bulk RNAseq. Differential gene expression, differences in microbiota composition, and metabolite abundance were determined. Gene and metabolite clusters were identified via weighted gene correlation network analysis and correlations with clinical and physiological parameters determined.

RESULTS: PI-IBS (59% female; 46 ± 2 years) and HV (64% female; 42 ± 2 years) demographics were comparable. Mean IBS-symptom severity score was 227; 94% were nonconstipation. Two- to 24-hour lactulose excretion was increased in PI-IBS, suggesting increased colonic permeability (4.4 ± 0.5 mg vs 2.6 ± 0.3 mg; P = .01). Colonic transit and sensory thresholds were similar between the 2 groups. Overall, expression of 2036 mucosal genes and 223 fecal metabolites were different, with changes more prominent in females. Fecal N-acetylputrescine was increased in PI-IBS and associated with colonic permeability, worse diarrhea, and negatively correlated with abundance of Collinsella aerofaciens. Histamine and N-acetylhistamine positively associated with 2- to 24-hour lactulose excretion. Eight weighted gene coexpression modules significantly correlated with phenotypes (sex, stool frequency, colonic permeability, transit).

CONCLUSIONS: Campylobacter PI-IBS patients demonstrate higher colonic permeability, which associated with changes in polyamine and histamine metabolites. Female patients demonstrated greater molecular changes.},
}

Humans
*Irritable Bowel Syndrome/metabolism/genetics/microbiology
Female
Male
Middle Aged
Adult
*Permeability
*Feces/chemistry/microbiology
*Colon/metabolism/microbiology
Gastrointestinal Microbiome/physiology
Transcriptome
Metabolomics/methods
Metabolome

@article {pmid40016544,
year = {2025},
author = {Zaminhan-Hassemer, M and Zagolin, GB and Aráujo, BC and Perazza, CA and Barbosa, DA and Menegidio, FB and Coutinho, LL and Tizioto, P and Hilsdorf, AWS},
title = {Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia.},
journal = {Veterinary research communications},
volume = {49},
number = {2},
pages = {120},
pmid = {40016544},
issn = {1573-7446},
mesh = {Animals ; *Propolis/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Cichlids/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; },
abstract = {The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m[3], comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.},
}

Animals
*Propolis/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Cichlids/microbiology
*Animal Feed/analysis
*Diet/veterinary
Dietary Supplements/analysis

@article {pmid40016229,
year = {2025},
author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2038},
pmid = {40016229},
issn = {2041-1723},
mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Agriculture/methods ; },
abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.},
}

*Oryza/microbiology/metabolism
*Nitrous Oxide/metabolism
*Rhizosphere
*Microbiota/genetics
*Soil Microbiology
*Nitrogen Fixation
*Plant Roots/microbiology/metabolism
Domestication
Metagenomics
Soil/chemistry
Nitrogenase/metabolism/genetics
Nitrogen/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Agriculture/methods

@article {pmid39923519,
year = {2025},
author = {Peng, Q and Cheng, S and Lin, J and Zheng, H and Xie, G},
title = {Metabolic and microbial functionality during the fermentation of traditional Amaranth stems: Insights from metagenomics, flavoromics, and metabolomics.},
journal = {Food chemistry},
volume = {474},
number = {},
pages = {143216},
doi = {10.1016/j.foodchem.2025.143216},
pmid = {39923519},
issn = {1873-7072},
mesh = {*Fermentation ; *Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Metagenomics ; *Flavoring Agents/metabolism/chemistry ; *Amaranthus/metabolism/chemistry ; Plant Stems/chemistry/microbiology/metabolism ; Taste ; },
abstract = {Fermented Amaranth stems is a traditional Chinese fermented vegetable known for its distinctive aroma, produced through natural microbial fermentation. However, the metabolic processes, flavor compounds, and microbial communities involved in its fermentation are not well understood. This study provides a comprehensive analysis using an integrated approach combining flavoromics, untargeted metabolomics, and metagenomics to examine the dynamic changes in metabolites and microbiota during fermentation. A total of 108 volatile organic compounds were identified, with sugar metabolism peaking on the third day of fermentation. The microbial community analysis revealed that key genera such as Pseudomonas, Acinetobacter, Pectobacterium, and Enterobacter play a significant role in flavor formation. The findings offer critical insights into the fermentation mechanisms and the production of flavor compounds, providing a foundation for optimizing fermentation processes and improving the flavor quality of fermented Amaranth stems. This research holds practical significance for enhancing food safety by controlling microbial communities during fermentation.},
}

*Fermentation
*Metabolomics
*Bacteria/metabolism/genetics/classification/isolation & purification
*Microbiota
*Volatile Organic Compounds/metabolism/chemistry/analysis
*Metagenomics
*Flavoring Agents/metabolism/chemistry
*Amaranthus/metabolism/chemistry
Plant Stems/chemistry/microbiology/metabolism
Taste

@article {pmid40015896,
year = {2025},
author = {Zheng, R and Peng, J and Li, Q and Liu, Y and Huang, D and Sheng, Y and Liu, C and Qi, L and Keyhani, NO and Tang, Q},
title = {Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides.},
journal = {Pesticide biochemistry and physiology},
volume = {208},
number = {},
pages = {106304},
doi = {10.1016/j.pestbp.2025.106304},
pmid = {40015896},
issn = {1095-9939},
mesh = {*Insecticides/pharmacology ; *Soil Microbiology ; *Metarhizium/genetics ; *Ivermectin/analogs & derivatives/pharmacology ; *Neonicotinoids/pharmacology ; Nitro Compounds/pharmacology ; Soil/chemistry ; Microbiota/drug effects ; },
abstract = {Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.},
}

*Insecticides/pharmacology
*Soil Microbiology
*Metarhizium/genetics
*Ivermectin/analogs & derivatives/pharmacology
*Neonicotinoids/pharmacology
Nitro Compounds/pharmacology
Soil/chemistry
Microbiota/drug effects

@article {pmid40008244,
year = {2025},
author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G},
title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae141},
pmid = {40008244},
issn = {2730-6151},
abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.},
}

@article {pmid40007605,
year = {2025},
author = {Buffet-Bataillon, S and Durão, G and Le Huërou-Luron, I and Rué, O and Le Cunff, Y and Cattoir, V and Bouguen, G},
title = {Gut microbiota dysfunction in Crohn's disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1540352},
pmid = {40007605},
issn = {2235-2988},
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Feces/microbiology ; Adult ; Female ; Male ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; Oxidative Stress ; Dysbiosis/microbiology ; Middle Aged ; Young Adult ; },
abstract = {INTRODUCTION: Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

METHODS: We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

RESULTS: As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

CONCLUSIONS: This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.},
}

*Crohn Disease/microbiology
Humans
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
*Metagenomics
*Feces/microbiology
Adult
Female
Male
Virulence Factors/genetics
Bacteria/classification/genetics/isolation & purification
Oxidative Stress
Dysbiosis/microbiology
Middle Aged
Young Adult

@article {pmid39933221,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Li, Y and Tu, Y and Wei, Y and Bai, J and Liu, Y},
title = {Gut microbiota causes depressive phenotype by modulating glycerophospholipid and sphingolipid metabolism via the gut-brain axis.},
journal = {Psychiatry research},
volume = {346},
number = {},
pages = {116392},
doi = {10.1016/j.psychres.2025.116392},
pmid = {39933221},
issn = {1872-7123},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Sphingolipids/metabolism ; Mice ; *Glycerophospholipids/metabolism ; Female ; Humans ; *Depression/metabolism/microbiology ; Pregnancy ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; Fecal Microbiota Transplantation ; Lipid Metabolism/physiology ; Phenotype ; Mice, Inbred C57BL ; },
abstract = {Emerging evidence suggests that changes in the gut microbiota (GM) are related to prenatal depression onset, but the underlying molecular mechanisms remain obscure. This study was conducted to explore how disordered GM is involved in the onset of prenatal depression through the microbiome-gut-brain (MGB) axis. We transplanted fecal microbiota from women with and without prenatal depression into germ-free mice. Fecal metagenomic sequencing and LC-MS untargeted metabolomics analysis were performed to identify the GM composition, function, and metabolites in mice. Lipid metabolomics analysis was then used to characterize the lipid metabolism of brain tissue in mice. We found that mice transplanted with fecal microbiota from women with prenatal depression exhibited depressive-like behaviors as well as characteristic disorders of the phylum Firmicutes. Weighted Gene Correlation Network Analysis identified three microbial and one metabolic module in the gut, alongside two lipid metabolic modules in the brain, as significantly related to all depressive-like behaviors. These modules were enriched for glycerophospholipid and sphingolipid metabolism. In addition, the GM of mice with depressive-like behaviors were enriched and deficient in relevant functions and enzymes in the glycerophospholipid (mainly phosphatidylethanolamine) and sphingolipid (mainly hexosyl-ceramide) metabolic pathways, respectively. Consistently, glycerophospholipid and sphingolipid metabolites in the brains of depressive-like mice were up- and down-regulated. Increased phosphatidylethanolamine and decreased hexosyl-ceramide were significantly related to differential genera in the gut. Collectively, our findings provide a novel microbial and metabolic framework for understanding the role of the MGB axis in prenatal depression, indicating that the GM may be involved in the onset of depressive phenotypes by modulating central glycerophospholipid and sphingolipid metabolic homeostasis.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Sphingolipids/metabolism
Mice
*Glycerophospholipids/metabolism
Female
Humans
*Depression/metabolism/microbiology
Pregnancy
*Brain-Gut Axis/physiology
*Brain/metabolism
Fecal Microbiota Transplantation
Lipid Metabolism/physiology
Phenotype
Mice, Inbred C57BL

@article {pmid39908139,
year = {2025},
author = {Zhang, Z and Guo, Q and Yang, Z and Sun, Y and Jiang, S and He, Y and Li, J and Zhang, J},
title = {Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia.},
journal = {Cell reports},
volume = {44},
number = {2},
pages = {115265},
doi = {10.1016/j.celrep.2025.115265},
pmid = {39908139},
issn = {2211-1247},
mesh = {Animals ; *Sarcopenia/metabolism/pathology ; *Niacin/pharmacology/metabolism ; Mice ; *Muscle, Skeletal/metabolism/drug effects ; Humans ; Forkhead Box Protein O3/metabolism ; Male ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism ; Mice, Inbred C57BL ; Muscle Proteins/metabolism ; Sirtuin 1/metabolism ; SKP Cullin F-Box Protein Ligases/metabolism ; Mitochondria, Muscle/metabolism/drug effects ; Ubiquitin-Protein Ligases/metabolism ; NAD/metabolism ; Gastrointestinal Microbiome/drug effects ; Mitochondria/metabolism/drug effects ; Female ; Cell Proliferation/drug effects ; Tripartite Motif Proteins ; },
abstract = {Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.},
}

Animals
*Sarcopenia/metabolism/pathology
*Niacin/pharmacology/metabolism
Mice
*Muscle, Skeletal/metabolism/drug effects
Humans
Forkhead Box Protein O3/metabolism
Male
Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism
Mice, Inbred C57BL
Muscle Proteins/metabolism
Sirtuin 1/metabolism
SKP Cullin F-Box Protein Ligases/metabolism
Mitochondria, Muscle/metabolism/drug effects
Ubiquitin-Protein Ligases/metabolism
NAD/metabolism
Gastrointestinal Microbiome/drug effects
Mitochondria/metabolism/drug effects
Female
Cell Proliferation/drug effects
Tripartite Motif Proteins

@article {pmid39894225,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HL and Chang, Y and Ryu, S and Kim, HN},
title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.},
journal = {Journal of affective disorders},
volume = {376},
number = {},
pages = {26-35},
doi = {10.1016/j.jad.2025.01.149},
pmid = {39894225},
issn = {1573-2517},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Fatty Acids, Volatile/metabolism ; Adult ; Middle Aged ; *Metagenomics/methods ; *Depression/microbiology/metabolism ; *Feces/microbiology/chemistry ; Faecalibacterium prausnitzii/metabolism/genetics ; Metagenome ; },
abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Cross-Sectional Studies
*Fatty Acids, Volatile/metabolism
Adult
Middle Aged
*Metagenomics/methods
*Depression/microbiology/metabolism
*Feces/microbiology/chemistry
Faecalibacterium prausnitzii/metabolism/genetics
Metagenome

@article {pmid38961050,
year = {2025},
author = {Bandeira, L and Faria, C and Cavalcante, F and Mesquita, A and Martins, C and Martins, S},
title = {Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.},
journal = {Folia microbiologica},
volume = {70},
number = {1},
pages = {159-175},
pmid = {38961050},
issn = {1874-9356},
support = {421350/2017-2//Instituto Chico Mendes de Conservação da Biodiversidade/ ; 18/2017//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Actinobacteria/chemistry/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/analysis ; Parks, Recreational ; Brazil ; *Soil Microbiology ; Biodiversity ; Soil/chemistry ; Metagenome ; },
abstract = {Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.},
}

*Actinobacteria/chemistry/classification/genetics/isolation & purification
DNA Barcoding, Taxonomic
RNA, Ribosomal, 16S/analysis
Parks, Recreational
Brazil
*Soil Microbiology
Biodiversity
Soil/chemistry
Metagenome

@article {pmid40006931,
year = {2025},
author = {Sarker, S and Talukder, S and Athukorala, A and Whiteley, PL},
title = {The Spleen Virome of Australia's Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/v17020176},
pmid = {40006931},
issn = {1999-4915},
mesh = {Animals ; *Phylogeny ; *Platypus/virology ; *Virome ; *Genome, Viral ; Australia ; *Papillomaviridae/genetics/classification/isolation & purification ; *Spleen/virology ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Genetic Variation ; },
abstract = {The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1-4) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus's evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.},
}

Animals
*Phylogeny
*Platypus/virology
*Virome
*Genome, Viral
Australia
*Papillomaviridae/genetics/classification/isolation & purification
*Spleen/virology
High-Throughput Nucleotide Sequencing
DNA, Viral/genetics
Genetic Variation

@article {pmid40005640,
year = {2025},
author = {Cao, X and Cui, Q and Li, D and Liu, Y and Liu, K and Li, Z},
title = {Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020273},
pmid = {40005640},
issn = {2076-2607},
support = {2022YSKY-57//Integrated analysis of soil hydrologic function of returning farmland to forest (grass) in Basic Scientific Research Youth Exploration Project of Central public welfare research Institute of Chinese Research Academy of Environmental Sciences, China/ ; },
abstract = {The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.},
}

@article {pmid40005401,
year = {2025},
author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A},
title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {2},
pages = {},
doi = {10.3390/medicina61020284},
pmid = {40005401},
issn = {1648-9144},
support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Female ; *Colitis, Ulcerative/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19 ; *Vitamins/therapeutic use ; Adult ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Probiotics/therapeutic use ; *SARS-CoV-2 ; Aged ; },
abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.},
}

Humans
Cross-Sectional Studies
Female
*Colitis, Ulcerative/drug therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects
*COVID-19
*Vitamins/therapeutic use
Adult
Middle Aged
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Probiotics/therapeutic use
*SARS-CoV-2
Aged

@article {pmid40005052,
year = {2025},
author = {Zang, P and Chen, P and Chen, J and Sun, J and Lan, H and Dong, H and Liu, W and Xu, N and Wang, W and Hou, L and Sun, B and Zhang, L and Huang, J and Wang, P and Ren, F and Liu, S},
title = {Alteration of Gastrointestinal Function and the Ameliorative Effects of Hericium erinaceus Polysaccharides in Tail Suspension Rats.},
journal = {Nutrients},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/nu17040724},
pmid = {40005052},
issn = {2072-6643},
support = {242300421105//Henan Natural Science Foundation of Excellent Young Scholars/ ; },
mesh = {Animals ; *Rats, Sprague-Dawley ; *Gastrointestinal Microbiome/drug effects ; *Hericium ; Rats ; Male ; *Polysaccharides/pharmacology ; Hindlimb Suspension ; Dysbiosis ; Dietary Supplements ; Gastrointestinal Tract/drug effects ; Gastrointestinal Diseases/drug therapy/prevention & control ; Weightlessness Simulation ; },
abstract = {Background/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.},
}

Animals
*Rats, Sprague-Dawley
*Gastrointestinal Microbiome/drug effects
*Hericium
Rats
Male
*Polysaccharides/pharmacology
Hindlimb Suspension
Dysbiosis
Dietary Supplements
Gastrointestinal Tract/drug effects
Gastrointestinal Diseases/drug therapy/prevention & control
Weightlessness Simulation

@article {pmid40004244,
year = {2025},
author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , },
title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041781},
pmid = {40004244},
issn = {1422-0067},
support = {LSHM20104; LSHM20068//Health Holland/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology ; *Feces/microbiology/virology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Aged ; *SARS-CoV-2/isolation & purification ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.},
}

Humans
*COVID-19/microbiology/virology
*Feces/microbiology/virology
Male
Female
*Gastrointestinal Microbiome/genetics
Middle Aged
Aged
*SARS-CoV-2/isolation & purification
Adult
Metagenome
Bacteria/classification/genetics/isolation & purification

@article {pmid40004174,
year = {2025},
author = {Cui, Y and Guan, H and Okyere, SK and Hua, Z and Deng, Y and Deng, H and Ren, Z and Deng, J},
title = {Microbial Guardians or Foes? Metagenomics Reveal Association of Gut Microbiota in Intestinal Toxicity Caused by DON in Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041712},
pmid = {40004174},
issn = {1422-0067},
support = {. 32273072//This research was supported by National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Trichothecenes/toxicity ; *Metagenomics/methods ; Cytokines/metabolism ; Intestinal Mucosa/metabolism/microbiology/pathology ; Zonula Occludens-1 Protein/metabolism/genetics ; Male ; Colon/microbiology/metabolism/pathology/drug effects ; Jejunum/microbiology/pathology/metabolism/drug effects ; Occludin/metabolism/genetics ; Intestines/microbiology/pathology/drug effects ; },
abstract = {The role of gut microbiota has become a research hotspot in recent years; however, whether the gut microbiota are involved in the alleviation or exacerbation of Deoxynivalenol (DON) toxicity has not been fully studied. Therefore, the objective of this study was to investigate whether the gut microbiota are involved in reducing or aggravating the intestinal damage induced by DON in mice. Mice that received or did not receive antibiotic-induced intestinal flora clearance were orally given DON (5 mg kg/bw/day) for 14 days. At the end of the experiment, serum, intestinal tissue samples and colon contents were collected for further analysis. DON caused development of severe histopathological damage, such as necrosis and inflammation of the jejunum and colon in mice without gut microbiota clearance. The levels of tight junction proteins ZO-1 and occludin were reduced in the jejunum and colon of mice without gut microbiota clearance. In addition, the mRNA and protein levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) were increased in mice without gut microbiota clearance. The presence of microbiota exacerbate the intestinal damage induced by DON via changes in gut microbiota abundance and production of gut damaging metabolites.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Trichothecenes/toxicity
*Metagenomics/methods
Cytokines/metabolism
Intestinal Mucosa/metabolism/microbiology/pathology
Zonula Occludens-1 Protein/metabolism/genetics
Male
Colon/microbiology/metabolism/pathology/drug effects
Jejunum/microbiology/pathology/metabolism/drug effects
Occludin/metabolism/genetics
Intestines/microbiology/pathology/drug effects

@article {pmid40003915,
year = {2025},
author = {Chao, X and Fan, Z and Wu, J and Ye, C and Wang, X and Li, R and Chen, S and Zhang, X and Fang, C and Luo, Q},
title = {Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041448},
pmid = {40003915},
issn = {1422-0067},
support = {2022B0202100002//Key-Area Research and Development Program of Guangdong Province/ ; 2024B03J1353//Science and Technology Program of Guangzhou City/ ; 2023ZD04064//STI2030-Major Projects/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Poultry Diseases/microbiology/genetics ; *Metagenomics/methods ; *Salmonella Infections, Animal/microbiology/genetics ; Cecum/microbiology ; RNA, Messenger/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Alternative Splicing ; Salmonella/genetics/pathogenicity ; RNA-Seq/methods ; Gene Expression Profiling ; Metagenome ; Gene Expression Regulation ; },
abstract = {The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.},
}

Animals
*Chickens/microbiology
*Poultry Diseases/microbiology/genetics
*Metagenomics/methods
*Salmonella Infections, Animal/microbiology/genetics
Cecum/microbiology
RNA, Messenger/genetics/metabolism
Gastrointestinal Microbiome/genetics
Alternative Splicing
Salmonella/genetics/pathogenicity
RNA-Seq/methods
Gene Expression Profiling
Metagenome
Gene Expression Regulation

@article {pmid40003912,
year = {2025},
author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P},
title = {Semen Microbiome, Male Infertility, and Reproductive Health.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041446},
pmid = {40003912},
issn = {1422-0067},
mesh = {Male ; Humans ; *Microbiota ; *Semen/microbiology ; *Infertility, Male/microbiology ; *Reproductive Health ; Female ; Reproductive Techniques, Assisted ; Spermatozoa/microbiology ; Fertility ; Pregnancy ; },
abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.},
}

Male
Humans
*Microbiota
*Semen/microbiology
*Infertility, Male/microbiology
*Reproductive Health
Female
Reproductive Techniques, Assisted
Spermatozoa/microbiology
Fertility
Pregnancy

@article {pmid40000989,
year = {2025},
author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P},
title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {90},
pmid = {40000989},
issn = {1471-2180},
support = {32201393//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; },
abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Humans
*Helicobacter pylori/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Helicobacter Infections/microbiology/drug therapy
*Gene Transfer, Horizontal
*Feces/microbiology
Mutation
Metagenomics
Klebsiella/genetics/drug effects
Female
Male
Genome, Bacterial/genetics
Adult
Escherichia/genetics/drug effects
Middle Aged
Genes, Bacterial/genetics

@article {pmid39998665,
year = {2025},
author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, Ł and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A},
title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {4},
pages = {110},
pmid = {39998665},
issn = {1432-0851},
support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Badań i Rozwoju/ ; },
mesh = {Humans ; *Melanoma/drug therapy/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lymphocytes/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Mycobiome ; Aged ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; Skin Neoplasms/immunology/drug therapy/microbiology ; Fungi/immunology ; },
abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.},
}

Humans
*Melanoma/drug therapy/immunology
*Gastrointestinal Microbiome/immunology/drug effects
Male
Female
Middle Aged
*Lymphocytes/immunology
*Immune Checkpoint Inhibitors/therapeutic use
*Mycobiome
Aged
Programmed Cell Death 1 Receptor/antagonists & inhibitors
Adult
Skin Neoplasms/immunology/drug therapy/microbiology
Fungi/immunology

@article {pmid39997957,
year = {2025},
author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N},
title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.},
journal = {Toxics},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/toxics13020142},
pmid = {39997957},
issn = {2305-6304},
abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.},
}

@article {pmid39950859,
year = {2025},
author = {Ma, Y and Zhang, M and Wang, Z and Cao, L and Li, Y and Wan, Z and Kane, Y and Wang, G and Li, X and Zhang, C},
title = {Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2467168},
doi = {10.1080/21505594.2025.2467168},
pmid = {39950859},
issn = {2150-5608},
mesh = {Humans ; *HIV Infections/drug therapy/virology/blood/immunology ; *Cytokines/blood ; *HIV-1/genetics/drug effects ; Male ; *Virome ; Adult ; Female ; Middle Aged ; Anti-Retroviral Agents/therapeutic use ; Metagenomics ; Anelloviridae/genetics ; Cohort Studies ; },
abstract = {An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.},
}

Humans
*HIV Infections/drug therapy/virology/blood/immunology
*Cytokines/blood
*HIV-1/genetics/drug effects
Male
*Virome
Adult
Female
Middle Aged
Anti-Retroviral Agents/therapeutic use
Metagenomics
Anelloviridae/genetics
Cohort Studies

@article {pmid39938296,
year = {2025},
author = {Tan, L and Liang, J and Qin, Z and Ning, T and Wei, X and Yang, B and Wang, Q and Xu, Y and Shen, F},
title = {Unveiling the sustained effects of plant root exudates on soil microbiome and resistome and the related functional traits.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124485},
doi = {10.1016/j.jenvman.2025.124485},
pmid = {39938296},
issn = {1095-8630},
mesh = {*Soil Microbiology ; *Plant Roots/microbiology/drug effects ; *Microbiota/drug effects ; *Rhizosphere ; *Plant Exudates ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/metabolism ; },
abstract = {Investigating the transmission mechanisms and influencing factors of antibiotic resistance genes (ARGs) in the soil-plant continuum is vital for mitigating ARG contamination and safeguarding plant and human health. Rhizosphere soil serves as a crucial interface for ARG propagation and transmission; however, it is unclear whether and how plant involved in regulating ARGs in their rhizosphere environment. Root exudates acting as vital links in the plant-soil-microbe interaction. Here, we examined the fluctuating patterns of the resistome and mobile genetic elements (MGEs) following exposure to four types of common root exudates: amino acids (AAs), sugars, long-chain organic acids (LCOAs), and short-chain organic acids (SCOAs). AAs exerted a rapid and pronounced effect, leading to a significant elevation in total ARG and MGE abundance by 3.18-fold and 21.06-fold, respectively, compared to the control group by day 7. Conversely, the impact of sugars manifested gradually over time. The influence of AAs and sugars persisted beyond 240 days post-treatment cessation. Importantly, the proliferation of ARGs was closely linked to the enrichment of plant growth-promoting bacteria (PGPBs) such as Pseudomonas, Cupriavidus, Azospirillum, Variovorax, and Ensifer. Functional analysis revealed that the potential features of ARGs and MGEs were associated with cell wall/membrane/envelope biogenesis, cell motility, and inorganic ion transport. This study offers novel insights into the factors influencing the dynamics of ARGs in the plant rhizosphere and may contribute to ecologically sustainable agricultural practices.},
}

*Soil Microbiology
*Plant Roots/microbiology/drug effects
*Microbiota/drug effects
*Rhizosphere
*Plant Exudates
Soil/chemistry
Drug Resistance, Microbial/genetics
Bacteria/genetics/drug effects/metabolism

@article {pmid39846163,
year = {2025},
author = {Jena, PK and Arditi, M and Noval Rivas, M},
title = {Gut Microbiota Alterations in Patients With Kawasaki Disease.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {45},
number = {3},
pages = {345-358},
doi = {10.1161/ATVBAHA.124.321201},
pmid = {39846163},
issn = {1524-4636},
support = {R01 HL139766/HL/NHLBI NIH HHS/United States ; R01 HL159297/HL/NHLBI NIH HHS/United States ; R01 HL149972/HL/NHLBI NIH HHS/United States ; R01 AI157274/AI/NIAID NIH HHS/United States ; R01 HL170580/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/immunology ; *Gastrointestinal Microbiome ; *Dysbiosis ; Animals ; Bacteria ; Risk Factors ; Feces/microbiology ; Host-Pathogen Interactions ; },
abstract = {The intestinal microbiota influences many host biological processes, including metabolism, intestinal barrier functions, and immune responses in the gut and distant organs. Alterations in its composition have been associated with the development of inflammatory disorders and cardiovascular diseases, including Kawasaki disease (KD). KD is an acute pediatric vasculitis of unknown etiology and the leading cause of acquired heart disease in children in the United States. The presence of gastrointestinal symptoms in the acute phase of KD has been associated with an increased risk of treatment resistance and the development of coronary artery aneurysms. Studies report alterations in fecal bacterial communities of patients with KD, characterized by the blooming of pathogenic bacteria and decreased relative abundance of short-chain fatty acid-producing bacteria. However, causality and functionality cannot be established from these observational patient cohorts of KD. This highlights the need for more advanced and rigorous studies to establish causality and functionality in both experimental models of KD vasculitis and patient cohorts. Here, we review the evidence linking an altered gut microbiota composition to the development of KD, assess the potential mechanisms involved in this process, and discuss the potential therapeutic value of these observations.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/immunology
*Gastrointestinal Microbiome
*Dysbiosis
Animals
Bacteria
Risk Factors
Feces/microbiology
Host-Pathogen Interactions

@article {pmid39997213,
year = {2025},
author = {Calado, R and Leal, MC and Silva, RXG and Borba, M and Ferro, A and Almeida, M and Madeira, D and Vieira, H},
title = {Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.},
journal = {Marine drugs},
volume = {23},
number = {2},
pages = {},
doi = {10.3390/md23020089},
pmid = {39997213},
issn = {1660-3397},
support = {UIDB/50017/2020 + UIDP/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; (Project Nº. C644915664-00000026)//"BLUE BIOECONOMY PACT", co-funded by the Next Gen-eration EU European Fund, under the incentive line "Agendas for Business Innovation" within Component 5-Capitalization and Business Innovation of the Portuguese Recovery and Resili-ence Plan (RRP), specifi/ ; },
mesh = {*Anthozoa/metabolism ; Animals ; *Coral Reefs ; *Biological Specimen Banks ; Bioprospecting ; Laboratories ; Humans ; Biological Products ; },
abstract = {Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.},
}

*Anthozoa/metabolism
Animals
*Coral Reefs
*Biological Specimen Banks
Bioprospecting
Laboratories
Humans
Biological Products

@article {pmid39991687,
year = {2025},
author = {Pan, Y and Jiao, FY},
title = {Helicobacter pylori infection and gastric microbiota: Insights into gastric and duodenal ulcer development.},
journal = {World journal of gastroenterology},
volume = {31},
number = {7},
pages = {100044},
pmid = {39991687},
issn = {2219-2840},
mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation & purification/genetics/pathogenicity ; *Duodenal Ulcer/microbiology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; *Gastric Mucosa/microbiology/pathology ; Metagenomics/methods ; Stomach/microbiology/pathology ; Dysbiosis/microbiology ; },
abstract = {Helicobacter pylori (H. pylori) infection plays a critical role in gastric diseases, impacting the microbiota structure in gastric and duodenal ulcers. In their study, Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls, revealing significant changes in microbial diversity and composition. This article reviews their findings, emphasizing H. pylori's role in gastric ulcers and the need for further research on its impact on duodenal ulcers. We evaluate the study's strengths and limitations, suggesting future research directions to enhance our understanding of H. pylori's contribution to ulcerative diseases.},
}

Humans
*Helicobacter Infections/microbiology
*Helicobacter pylori/isolation & purification/genetics/pathogenicity
*Duodenal Ulcer/microbiology
*Gastrointestinal Microbiome
*Stomach Ulcer/microbiology
*Gastric Mucosa/microbiology/pathology
Metagenomics/methods
Stomach/microbiology/pathology
Dysbiosis/microbiology

@article {pmid39991683,
year = {2025},
author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C},
title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.},
journal = {World journal of gastroenterology},
volume = {31},
number = {7},
pages = {100051},
pmid = {39991683},
issn = {2219-2840},
mesh = {Humans ; Indonesia/epidemiology ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; *Colonoscopy ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Metagenomics/methods ; Bacteria/isolation & purification/genetics/classification ; },
abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.

AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.

METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).

RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.

CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).},
}

Humans
Indonesia/epidemiology
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Case-Control Studies
*Colonoscopy
*Colon/microbiology
*Intestinal Mucosa/microbiology
*RNA, Ribosomal, 16S/genetics
Aged
Adult
Metagenomics/methods
Bacteria/isolation & purification/genetics/classification

@article {pmid39919360,
year = {2025},
author = {Lemons, JMS and Narrowe, AB and Firrman, J and Mahalak, KK and Liu, L and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P},
title = {The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo.},
journal = {Food chemistry},
volume = {473},
number = {},
pages = {143037},
doi = {10.1016/j.foodchem.2025.143037},
pmid = {39919360},
issn = {1873-7072},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Butylated Hydroxyanisole/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification/metabolism ; Adult ; *Food Additives/pharmacology ; Infant ; Middle Aged ; Aged ; Young Adult ; Child, Preschool ; Child ; Female ; Adolescent ; Male ; },
abstract = {Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Butylated Hydroxyanisole/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification/metabolism
Adult
*Food Additives/pharmacology
Infant
Middle Aged
Aged
Young Adult
Child, Preschool
Child
Female
Adolescent
Male

@article {pmid39909332,
year = {2025},
author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J},
title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125787},
doi = {10.1016/j.envpol.2025.125787},
pmid = {39909332},
issn = {1873-6424},
mesh = {*Cadmium/metabolism ; *Glycine max/genetics/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Metagenomics ; Metagenome ; Multiomics ; },
abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.},
}

*Cadmium/metabolism
*Glycine max/genetics/microbiology/metabolism
*Rhizosphere
*Soil Pollutants/metabolism
*Soil Microbiology
*Microbiota
Soil/chemistry
Biodegradation, Environmental
Bacteria/genetics/metabolism
Metagenomics
Metagenome
Multiomics

@article {pmid39887086,
year = {2025},
author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L},
title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.},
journal = {Journal of Crohn's & colitis},
volume = {19},
number = {2},
pages = {},
doi = {10.1093/ecco-jcc/jjaf018},
pmid = {39887086},
issn = {1876-4479},
support = {4100068710//Commonwealth Universal Research Enhancement/ ; 693867//Crohn's and Colitis Foundation Career Development Award/ ; },
mesh = {Humans ; *Crohn Disease/microbiology ; Male ; Child ; Female ; Cross-Sectional Studies ; Adolescent ; *Feces/microbiology ; *Escherichia coli/isolation & purification ; *Gastrointestinal Microbiome/physiology ; Diet/adverse effects/methods ; Case-Control Studies ; Virulence ; Metabolome ; Inflammation/microbiology ; },
abstract = {BACKGROUND AND AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, the relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.

METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the mC-DII, and diet quality was assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean Eating Index (aMed). The microbiome was analyzed using shotgun metagenomic sequencing and untargeted metabolomic analysis.

RESULTS: A poor-quality, pro-inflammatory diet, with similar mC-DII, HEI-2015, and aMed scores, was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential, and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. A positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins, and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.

CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.},
}

Humans
*Crohn Disease/microbiology
Male
Child
Female
Cross-Sectional Studies
Adolescent
*Feces/microbiology
*Escherichia coli/isolation & purification
*Gastrointestinal Microbiome/physiology
Diet/adverse effects/methods
Case-Control Studies
Virulence
Metabolome
Inflammation/microbiology

@article {pmid39550746,
year = {2025},
author = {Karaca, C and Takcı, HAM},
title = {Role of gut microbiome in developing necrotizing enterocolitis.},
journal = {Folia microbiologica},
volume = {70},
number = {1},
pages = {197-204},
pmid = {39550746},
issn = {1874-9356},
support = {21-13192//Kilis 7 Aralık University of Research Project Committee/ ; },
mesh = {*Enterocolitis, Necrotizing/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Male ; Metagenomics ; Female ; High-Throughput Nucleotide Sequencing ; Infant, Premature ; DNA, Bacterial/genetics ; },
abstract = {Necrotizing enterocolitis (NEC) is one of the most devastating intestinal diseases observed in preterm in the first days of life. Researchers have recently focused on potential predictive biomarkers for early and concomitant diagnoses. Thus, we inquired about the linkage of intestinal dysbiosis, one of the most important factors in NEC development to the gut microbiota. In this study, the systematic differences in the bacterial composition between neonates affected by NEC and healthy newborns were highlighted by metagenomic analysis. The next-generation sequencing of the V3-V4 variable region of the 16S rRNA gene and gene-specific qPCR analyzed the untargeted gut microbiota. Total bacteria, total and fecal coliform loads in stool samples with NEC were higher than control. OTU-level relative abundances of NEC infant was characterized by Firmicutes and Bacteroidetes at phylum levels. At the genus level, NEC stool was identified by the lack of Klebsiella and the presence of Roseburia, Blautia, and Parasutterella. Finally, Clostridium fessum was the predominant species of Clostridium genus in disease and healthy specimens at the species level, whereas Clostridium jeddahitimonense was at NEC diagnosis. Despite a strong relationship between pathophysiology and characterization of gut microbiota at a clinical diagnosis of NEC, our results emphasize the broad difficulty in identifying potential biomarkers.},
}

*Enterocolitis, Necrotizing/microbiology
*Gastrointestinal Microbiome
Humans
Infant, Newborn
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Male
Metagenomics
Female
High-Throughput Nucleotide Sequencing
Infant, Premature
DNA, Bacterial/genetics

@article {pmid39986751,
year = {2025},
author = {Wang, C and Zhao, J and Zhao, W and Xue, L and Chen, Y and Tian, J and Wang, H and Ji, X and Tian, X and Zhang, J and Gu, Y},
title = {A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {204},
number = {},
pages = {115859},
doi = {10.1016/j.foodres.2025.115859},
pmid = {39986751},
issn = {1873-7145},
mesh = {Animals ; Cattle ; *Caseins/metabolism ; *Metabolomics ; *Metagenomics ; Female ; Rumen/microbiology/metabolism ; Gastrointestinal Microbiome ; Milk/microbiology ; Bacteria/metabolism/classification/genetics ; Genotype ; },
abstract = {β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.},
}

Animals
Cattle
*Caseins/metabolism
*Metabolomics
*Metagenomics
Female
Rumen/microbiology/metabolism
Gastrointestinal Microbiome
Milk/microbiology
Bacteria/metabolism/classification/genetics
Genotype

@article {pmid39986042,
year = {2025},
author = {Bacha, LF and Oliveira, MAP and Landuci, F and Vicente, AC and Paz, PH and Lima, M and Hilário, M and Campos, LS and Thompson, M and Chueke, C and Tschoeke, D and Ottoni, A and Teixera, LM and Cosenza, C and de Souza, W and de Rezende, C and Thompson, C and Thompson, F},
title = {Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178778},
doi = {10.1016/j.scitotenv.2025.178778},
pmid = {39986042},
issn = {1879-1026},
abstract = {Baia da Ilha Grande (BIG), Rio de Janeiro, Brazil, is one of the largest bays in the world. BIG is important because it serves as a route for the mining and oil industries and plays a vital role in mariculture activities. However, BIG has suffered significant impacts in recent years due to increased pollution and climate change, culminating in a local mariculture collapse. We examined the pollution levels of the bay. Biogeochemical, microbiological, and metagenomics analyses were conducted in ten rivers during the 2022 dry and rainy seasons. Combined data analyses showed that the bay's ten most significant rivers are polluted and classified into three decreasing levels of pollution groups (P1-P3). The P1 group (Centro, Japuíba, Jacuecanga) had the worst-case scenario for all pollution types, and the highest number of the nearby populations, nautical workshops and hospitals. Whereas the P2 (Jacarei, Perequeaçu and Taquari) and P3 (Frade, Bracuí, Mambucaba, São Roque) had relatively reduced pollution, as shown mainly by fecal bacteria. Metals, such as Al (>0.3 mg/L), Fe (>1.4 mg/L), Pb (>0.15 mg/L), and resistance genes (∼2 % metagenomic profile) were also more abundant in P1. High levels of metals and antibiotic resistance genes were a strong indication of pollution. The results from this study shed light on the health status of BIG rivers for further conservation programs and public policies to prevent rivers and marine biodiversity losses, and they serves as a warning on the urgent need to treat effluents in the region.},
}

@article {pmid39923290,
year = {2025},
author = {Wang, S and Wu, M},
title = {Decoding the link between microbial secondary metabolites and colorectal cancer.},
journal = {Computational biology and chemistry},
volume = {115},
number = {},
pages = {108372},
doi = {10.1016/j.compbiolchem.2025.108372},
pmid = {39923290},
issn = {1476-928X},
mesh = {*Colorectal Neoplasms/metabolism/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {Colorectal cancer (CRC) is a prevalent form of cancer in humans, with the gut microbiota playing a significant role in its pathogenesis. Although previous research has primarily focused on the role of primary metabolites produced by gut microbes in CRC development, the role of secondary metabolites remains largely unexplored. Secondary metabolites are known to mediate crucial interactions between the microbiota and the host, potentially influencing CRC progression. However, their specific relationship to CRC pathogenesis is poorly understood. To address this gap, we performed a meta-analysis using fecal metagenomic data from a cohort of CRC patients and healthy controls, aiming to identify CRC-associated microbial secondary metabolite biosynthetic gene clusters (BGCs). Our findings not only provide valuable insights into the pathogenicity and carcinogenicity of CRC but also shed light on the potential mechanisms underlying its development.},
}

*Colorectal Neoplasms/metabolism/microbiology
Humans
*Gastrointestinal Microbiome
Feces/microbiology

@article {pmid39954350,
year = {2025},
author = {Dong, Y and Liu, H and Habimana, O},
title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.},
journal = {International journal of food microbiology},
volume = {432},
number = {},
pages = {111098},
doi = {10.1016/j.ijfoodmicro.2025.111098},
pmid = {39954350},
issn = {1879-3460},
mesh = {*Vibrio/genetics/drug effects/isolation & purification ; *Seafood/microbiology ; China ; Animals ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; Humans ; Food Contamination/analysis ; Microbiota ; Biofilms/growth & development ; Food Safety ; },
abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.},
}

*Vibrio/genetics/drug effects/isolation & purification
*Seafood/microbiology
China
Animals
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Food Microbiology
Humans
Food Contamination/analysis
Microbiota
Biofilms/growth & development
Food Safety

@article {pmid39947314,
year = {2025},
author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L},
title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.},
journal = {Life sciences},
volume = {365},
number = {},
pages = {123462},
doi = {10.1016/j.lfs.2025.123462},
pmid = {39947314},
issn = {1879-0631},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Microbiota/physiology ; *Mouth/microbiology ; Fusobacterium nucleatum/pathogenicity ; Porphyromonas gingivalis/pathogenicity ; Animals ; },
abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.},
}

Humans
*Colorectal Neoplasms/microbiology
*Microbiota/physiology
*Mouth/microbiology
Fusobacterium nucleatum/pathogenicity
Porphyromonas gingivalis/pathogenicity
Animals

@article {pmid39824262,
year = {2025},
author = {Özdemir, A and Sarzhanov, F and Doğruman-Al, F and Gündoğdu, A and Nalbantoğlu, U and Yozgat, A and Yıldız, BD and Büyüktuncer, Z},
title = {Exploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107306},
doi = {10.1016/j.micpath.2025.107306},
pmid = {39824262},
issn = {1096-1208},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; *Blastocystis/isolation & purification/genetics/classification ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Female ; Middle Aged ; Blastocystis Infections/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; DNA, Bacterial/genetics ; Gastrectomy ; },
abstract = {This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).},
}

Humans
*Gastrointestinal Microbiome
*Bariatric Surgery
*Obesity, Morbid/surgery/microbiology
*Blastocystis/isolation & purification/genetics/classification
Male
*RNA, Ribosomal, 16S/genetics
Adult
Female
Middle Aged
Blastocystis Infections/microbiology/parasitology
Bacteria/classification/genetics/isolation & purification
Feces/microbiology/parasitology
DNA, Bacterial/genetics
Gastrectomy

@article {pmid39985639,
year = {2025},
author = {Zhang, N and Tran, S and Moskatel, LS},
title = {The Gut Microbiome and Migraine: Updates in Understanding.},
journal = {Current neurology and neuroscience reports},
volume = {25},
number = {1},
pages = {20},
pmid = {39985639},
issn = {1534-6293},
mesh = {Humans ; *Migraine Disorders/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; },
abstract = {PURPOSE OF REVIEW: We provide an overview of the field of microbiome research, the current understanding of the microbiome-gut-brain axis, and the most recent updates on the interplay between migraine and the gut microbiome.

RECENT FINDINGS: Pre-clinical studies suggest that gut microbiota is required for normal pain sensation. There is also evidence in rodent models that there is potential application of food, herbal medicines, probiotics, and short chain fatty acids (SCFAs) as novel therapies for migraine. Evidence from human cohorts suggests that there is altered gut microbiota in people with migraine, and that the microbiome dysbiosis is from both compositional and functional aspects. Recent metagenome-wide association studies (MWAS) that employ Mendelian Randomization support the causal association between gut microbiota and migraine. The connection between migraine and the gut microbiome remains underexplored, but recent preclinical and clinical studies support the association between gut microbiota and the development of migraine.},
}

Humans
*Migraine Disorders/microbiology
*Gastrointestinal Microbiome/physiology
Animals
*Brain-Gut Axis/physiology
Dysbiosis/microbiology
Probiotics/therapeutic use

@article {pmid39984934,
year = {2025},
author = {Chen, X and Wei, J and Zhang, L and Wang, H and Zhang, Y and Li, Z and Wang, X and Liu, L and Zhang, Y and Zhang, T},
title = {Association between plasma short-chain fatty acids and inflammation in human immunodeficiency virus-associated neurocognitive disorder: a pilot study.},
journal = {Lipids in health and disease},
volume = {24},
number = {1},
pages = {66},
pmid = {39984934},
issn = {1476-511X},
support = {7222091//Natural Science Foundation of Beijing Municipality/ ; 81873761//National Natural Science Foundation of China/ ; 82241072, 82072271//National Natural Science Foundation of China/ ; 7222095//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *Fatty Acids, Volatile/blood ; Male ; Female ; Pilot Projects ; Middle Aged ; *Gastrointestinal Microbiome ; *Inflammation/blood ; Adult ; Cytokines/blood ; HIV Infections/blood/complications/virology ; Biomarkers/blood ; Neurocognitive Disorders/blood/virology ; Cognitive Dysfunction/blood ; Case-Control Studies ; ROC Curve ; },
abstract = {BACKGROUND AND AIMS: Short-chain fatty acids (SCFAs), key metabolites produced by gut microbiota, have neuroprotective effects in neurodegenerative diseases by modulating immune responses. However, their role in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains largely unexplored.

METHODS: We recruited HAND patients, HIV Control, and healthy controls (HC). Plasma SCFAs and SCFA-producing gut microbiota were quantified via gas chromatography-mass spectrometry and fecal metagenomic analysis. Inflammatory cytokine levels were measured using liquid chromatography. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive accuracy of SCFAs for HAND.

RESULTS: Plasma SCFAs were significantly reduced in HAND patients, correlating with a decrease in SCFA-producing gut bacteria, such as Prevotella and its related species. Reduced SCFAs were positively correlated with pro-inflammatory cytokines and cognitive impairment, while being negatively correlated with anti-inflammatory cytokines. ROC curve analysis demonstrated that several SCFAs exhibited strong predictive accuracy for HAND status.

CONCLUSIONS: SCFAs may influence cognitive function by modulating inflammatory responses, and identifies plasma SCFAs as potential biomarkers and therapeutic targets for HAND. Further investigation is needed to delineate the mechanisms that SCFAs influence HAND pathology.},
}

Humans
*Fatty Acids, Volatile/blood
Male
Female
Pilot Projects
Middle Aged
*Gastrointestinal Microbiome
*Inflammation/blood
Adult
Cytokines/blood
HIV Infections/blood/complications/virology
Biomarkers/blood
Neurocognitive Disorders/blood/virology
Cognitive Dysfunction/blood
Case-Control Studies
ROC Curve

@article {pmid39980208,
year = {2025},
author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K},
title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14086},
doi = {10.1111/1755-0998.14086},
pmid = {39980208},
issn = {1755-0998},
support = {856488//H2020 European Research Council/ ; },
abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.},
}

@article {pmid39979617,
year = {2025},
author = {Ohlsson, C and Lawenius, L and Jiang, Y and Horkeby, K and Wu, J and Nilsson, KH and Koskela, A and Tuukkanen, J and Movérare-Skrtic, S and Henning, P and Sjögren, K},
title = {The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6182},
pmid = {39979617},
issn = {2045-2322},
mesh = {Animals ; Female ; *Probiotics/pharmacology/administration & dosage ; Mice ; *Bone Density/drug effects ; Diet, High-Fat/adverse effects ; Bone and Bones/drug effects ; Mice, Inbred C57BL ; Ovariectomy ; Gastrointestinal Microbiome/drug effects ; Diet ; },
abstract = {Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.},
}

Animals
Female
*Probiotics/pharmacology/administration & dosage
Mice
*Bone Density/drug effects
Diet, High-Fat/adverse effects
Bone and Bones/drug effects
Mice, Inbred C57BL
Ovariectomy
Gastrointestinal Microbiome/drug effects
Diet

@article {pmid39938449,
year = {2025},
author = {Ye, L and Yao, Z and Xuan, Q and Liu, Q and Bo, T},
title = {The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.},
journal = {Biochemical and biophysical research communications},
volume = {752},
number = {},
pages = {151466},
doi = {10.1016/j.bbrc.2025.151466},
pmid = {39938449},
issn = {1090-2104},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Gastrectomy ; *Homeostasis ; *Mice, Inbred C57BL ; Mice ; Male ; Fatty Liver/metabolism/pathology ; Disease Models, Animal ; },
abstract = {The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.},
}

Animals
*Gastrointestinal Microbiome
*Gastrectomy
*Homeostasis
*Mice, Inbred C57BL
Mice
Male
Fatty Liver/metabolism/pathology
Disease Models, Animal

@article {pmid39490771,
year = {2025},
author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJY and Yu, J},
title = {Multi-Cohort Analysis Reveals Altered Archaea in Colorectal Cancer Fecal Samples Across Populations.},
journal = {Gastroenterology},
volume = {168},
number = {3},
pages = {525-538.e2},
doi = {10.1053/j.gastro.2024.10.023},
pmid = {39490771},
issn = {1528-0012},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/diagnosis ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; *Adenoma/microbiology/genetics ; Female ; Middle Aged ; Case-Control Studies ; Metagenomics ; Aged ; Archaea/genetics/isolation & purification ; Metagenome ; Biomarkers, Tumor/genetics/analysis ; Cohort Studies ; },
abstract = {BACKGROUND & AIMS: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts across 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls [HCs]). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria, as well as methanogenic functions were analyzed. A Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HCs, patients with adenoma, to patients with CRC with the Methanobacteriota phylum enriched while the order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, whereas 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in patients with CRC across multiple cohorts. Among them, M stadtmanae, Methanobrevibacter_A sp900314695, and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in patients with CRC. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating patients with CRC from healthy individuals with the area under the curve ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, patients with adenoma, and patients with CRC. Archaeal biomarkers, combined with bacterial features, have potential as noninvasive diagnostic biomarkers for CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics/diagnosis
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Male
*Adenoma/microbiology/genetics
Female
Middle Aged
Case-Control Studies
Metagenomics
Aged
Archaea/genetics/isolation & purification
Metagenome
Biomarkers, Tumor/genetics/analysis
Cohort Studies

@article {pmid39128495,
year = {2025},
author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C},
title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.},
journal = {The Journal of investigative dermatology},
volume = {145},
number = {3},
pages = {605-617.e14},
doi = {10.1016/j.jid.2024.07.020},
pmid = {39128495},
issn = {1523-1747},
mesh = {Humans ; *Psoriasis/microbiology/genetics ; Male ; Female ; *Metagenome ; Adult ; *Scalp/microbiology ; Middle Aged ; Microbiota/genetics ; Scalp Dermatoses/microbiology/genetics ; Metagenomics/methods ; },
abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.},
}

Humans
*Psoriasis/microbiology/genetics
Male
Female
*Metagenome
Adult
*Scalp/microbiology
Middle Aged
Microbiota/genetics
Scalp Dermatoses/microbiology/genetics
Metagenomics/methods

@article {pmid39979340,
year = {2025},
author = {Di Costanzo, F and Di Marsico, M and Orefice, I and Kristoffersen, JB and Kasapidis, P and Chaumier, T and Ambrosino, L and Miralto, M and Aiese Cigliano, R and Verret, F and Tirichine, L and Trindade, M and Van Zyl, L and Di Dato, V and Romano, G},
title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {310},
pmid = {39979340},
issn = {2052-4463},
mesh = {*Diatoms/genetics ; Genome ; Molecular Sequence Annotation ; DNA Methylation ; Transcriptome ; DNA Transposable Elements ; Metagenome ; },
abstract = {Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.},
}

*Diatoms/genetics
Genome
Molecular Sequence Annotation
DNA Methylation
Transcriptome
DNA Transposable Elements
Metagenome

@article {pmid39903699,
year = {2025},
author = {Roothans, N and van Loosdrecht, MCM and Laureni, M},
title = {Metabolic labour division trade-offs in denitrifying microbiomes.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf020},
pmid = {39903699},
issn = {1751-7370},
support = {JG191217009/732.750/CU//Stichting Toegepast Onderzoek Waterbeheer/ ; 20.0787440//Hoogheemraadschap Hollands Noorderkwartier/ ; Z62737/U131154//Waterschap de Dommel/ ; },
mesh = {*Denitrification ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Nitrates/metabolism ; Nitrites/metabolism ; Metagenome ; Ecosystem ; },
abstract = {Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.},
}

*Denitrification
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
Nitrates/metabolism
Nitrites/metabolism
Metagenome
Ecosystem

@article {pmid39893570,
year = {2025},
author = {Zampieri, G and Santinello, D and Palù, M and Orellana, E and Costantini, P and Favaro, L and Campanaro, S and Treu, L},
title = {Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf017},
pmid = {39893570},
issn = {1751-7370},
mesh = {*Carbon Dioxide/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Microbiota ; Formates/metabolism ; Acetates/metabolism ; Hydrogen/metabolism ; Methanobacteriaceae/metabolism/genetics ; Metagenome ; Oxidation-Reduction ; },
abstract = {Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by Sphaerobacter thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.},
}

*Carbon Dioxide/metabolism
*Methane/metabolism
Anaerobiosis
*Microbiota
Formates/metabolism
Acetates/metabolism
Hydrogen/metabolism
Methanobacteriaceae/metabolism/genetics
Metagenome
Oxidation-Reduction

@article {pmid39837331,
year = {2025},
author = {Valdés-Mas, R and Leshem, A and Zheng, D and Cohen, Y and Kern, L and Zmora, N and He, Y and Katina, C and Eliyahu-Miller, S and Yosef-Hevroni, T and Richman, L and Raykhel, B and Allswang, S and Better, R and Shmueli, M and Saftien, A and Cullin, N and Slamovitz, F and Ciocan, D and Ouyang, KS and Mor, U and Dori-Bachash, M and Molina, S and Levin, Y and Atarashi, K and Jona, G and Puschhof, J and Harmelin, A and Stettner, N and Chen, M and Suez, J and Honda, K and Lieb, W and Bang, C and Kori, M and Maharshak, N and Merbl, Y and Shibolet, O and Halpern, Z and Shouval, DS and Shamir, R and Franke, A and Abdeen, SK and Shapiro, H and Savidor, A and Elinav, E},
title = {Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.},
journal = {Cell},
volume = {188},
number = {4},
pages = {1062-1083.e36},
doi = {10.1016/j.cell.2024.12.016},
pmid = {39837331},
issn = {1097-4172},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; Animals ; *Proteomics/methods ; *Feces/microbiology/chemistry ; Mice ; *Metagenome ; *Diet ; Dysbiosis/microbiology ; Exposome ; Female ; Male ; Mice, Inbred C57BL ; Biomarkers/metabolism ; },
abstract = {Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
Animals
*Proteomics/methods
*Feces/microbiology/chemistry
Mice
*Metagenome
*Diet
Dysbiosis/microbiology
Exposome
Female
Male
Mice, Inbred C57BL
Biomarkers/metabolism

@article {pmid39970096,
year = {2024},
author = {Begmatov, SA and Beletsky, AV and Rakitin, AL and Lukina, AP and Sokolyanskaya, LO and Rakitin, AV and Glukhova, LB and Mardanov, AV and Karnachuk, OV and Ravin, NV},
title = {[Antibiotic Resistance Genes in Cattle Gut Microbiota: Influence of Housing Conditions].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {996-1006},
pmid = {39970096},
issn = {0026-8984},
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Housing, Animal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics/drug effects ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; },
abstract = {Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of the feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides, and streptogramins), phenicols, and tetracyclines were detected in samples from both groups of animals, the content of the resistome in the fecal microbiome of stall-bred cattle was about ten times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, the content of which in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.},
}

Animals
Cattle
*Gastrointestinal Microbiome/drug effects/genetics
*Feces/microbiology
Anti-Bacterial Agents/pharmacology
Housing, Animal
Genes, Bacterial
Drug Resistance, Bacterial/genetics/drug effects
beta-Lactams/pharmacology
beta-Lactamases/genetics

@article {pmid39969428,
year = {2025},
author = {Bloom, PP and Bassis, CM and Crossette, E and Silber, JL and Norman, JM and Young, VB and Lok, ASF},
title = {Safety and efficacy of a defined bacterial consortium, VE303, to treat HE.},
journal = {Hepatology communications},
volume = {9},
number = {3},
pages = {},
doi = {10.1097/HC9.0000000000000650},
pmid = {39969428},
issn = {2471-254X},
mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects ; *Hepatic Encephalopathy/drug therapy ; Aged ; Treatment Outcome ; Vancomycin/therapeutic use/adverse effects ; Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage ; Feces/microbiology/chemistry ; Lactulose/therapeutic use ; Rifaximin/therapeutic use ; Adult ; },
abstract = {BACKGROUND: Novel therapies are needed to treat HE, and microbiome modulation is a promising target. VE303 is a defined consortium of 8 purified, clonal bacterial strains, known to produce metabolites that may be beneficial in HE. We evaluated the safety and efficacy of VE303 to treat HE.

METHODS: We performed a single-center, randomized, placebo-controlled trial of VE303 in adult patients with a history of overt HE (NCT04899115). Eligible patients were taking lactulose and rifaximin, had no recent systemic antibiotics, and had MELD ≤20. All patients received 5 days of oral vancomycin followed by randomization to 14 days of VE303 or placebo (2:1). The primary endpoints were incidence of serious adverse events and change in psychometric HE score (PHES) from baseline to 4 weeks after treatment. Stool samples underwent metagenomic sequencing and metabolite quantification.

RESULTS: Eighteen patients completed the trial, 56% men, with a mean age of 59 years and a mean MELD of 11. Patients who received VE303 had a mean change in PHES of +1.5 versus -1.0 in those who received a placebo (p=0.20). Two of the 12 patients who received VE303 had at least 1 serious adverse event (all overt HE hospitalizations), compared with 0/6 patients who received a placebo. In the patients who received VE303, 2 of 8 strains engrafted in >50% of patients. Both VE303 strain engraftment and increased stool butyrate production had a trend toward improved PHES.

CONCLUSIONS: VE303 was well tolerated in patients with cirrhosis and a history of overt HE, leading to the engraftment of certain VE303 strains and a higher percentage of patients with improved PHES.},
}

Humans
Male
Middle Aged
Female
*Gastrointestinal Microbiome/drug effects
*Hepatic Encephalopathy/drug therapy
Aged
Treatment Outcome
Vancomycin/therapeutic use/adverse effects
Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage
Feces/microbiology/chemistry
Lactulose/therapeutic use
Rifaximin/therapeutic use
Adult

@article {pmid39947184,
year = {2025},
author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I},
title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.},
journal = {Cell systems},
volume = {16},
number = {2},
pages = {101196},
doi = {10.1016/j.cels.2025.101196},
pmid = {39947184},
issn = {2405-4720},
mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Metabolic Networks and Pathways/genetics ; Machine Learning ; Metagenome/genetics ; Genome, Microbial ; },
abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.},
}

Humans
*Microbiota/genetics
Metagenomics/methods
Metabolic Networks and Pathways/genetics
Machine Learning
Metagenome/genetics
Genome, Microbial

@article {pmid39690119,
year = {2025},
author = {Di Gloria, L and Baldi, S and Curini, L and Bertorello, S and Nannini, G and Cei, F and Niccolai, E and Ramazzotti, M and Amedei, A},
title = {Experimental tests challenge the evidence of a healthy human blood microbiome.},
journal = {The FEBS journal},
volume = {292},
number = {4},
pages = {796-808},
doi = {10.1111/febs.17362},
pmid = {39690119},
issn = {1742-4658},
support = {//Ministry of University and Research (MUR)/ ; //FONZIE project (CUP B55F21007810001)/ ; //National Recovery and Resilience Plan (NRRP)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *DNA, Bacterial/genetics/blood ; Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Blood/microbiology ; Sequence Analysis, DNA/methods ; Healthy Volunteers ; Female ; Male ; Adult ; },
abstract = {The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.},
}

Humans
*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
*DNA, Bacterial/genetics/blood
Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Blood/microbiology
Sequence Analysis, DNA/methods
Healthy Volunteers
Female
Male
Adult

@article {pmid39578945,
year = {2025},
author = {Li, D and Zhi, J and Ye, J and Yue, W and Yang, Y},
title = {Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis.},
journal = {Environmental entomology},
volume = {54},
number = {1},
pages = {119-129},
doi = {10.1093/ee/nvae117},
pmid = {39578945},
issn = {1938-2936},
support = {[2016] 5802//Guizhou International Science and Technology Cooperation Base/ ; },
mesh = {Diet ; Gastrointestinal Microbiome ; Metagenome ; Phaseolus ; Rosa ; Sequence Analysis, DNA ; *Thysanoptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.},
}

Diet
Gastrointestinal Microbiome
Metagenome
Phaseolus
Rosa
Sequence Analysis, DNA
*Thysanoptera/microbiology
*Bacteria/classification/genetics/isolation & purification

@article {pmid39967175,
year = {2025},
author = {Aragão, MOP and Lima, FR and Passamani, FRF and Santos, MAA and Rezende, JP and Batista, LR},
title = {Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil.},
journal = {Food research international (Ottawa, Ont.)},
volume = {202},
number = {},
pages = {115724},
doi = {10.1016/j.foodres.2025.115724},
pmid = {39967175},
issn = {1873-7145},
mesh = {*Cheese/microbiology ; Brazil ; *Food Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Animals ; Microbiota/genetics ; Geotrichum/genetics ; Milk/microbiology ; Biodiversity ; Cattle ; Lactococcus/genetics/isolation & purification/classification ; },
abstract = {Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.},
}

*Cheese/microbiology
Brazil
*Food Microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
Animals
Microbiota/genetics
Geotrichum/genetics
Milk/microbiology
Biodiversity
Cattle
Lactococcus/genetics/isolation & purification/classification

@article {pmid39967137,
year = {2025},
author = {Espí-Malillos, A and López-Almela, I and Ruiz-García, P and López-Mendoza, MC and Carrón, N and González-Torres, P and Quereda, JJ},
title = {Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination.},
journal = {Food research international (Ottawa, Ont.)},
volume = {202},
number = {},
pages = {115637},
doi = {10.1016/j.foodres.2024.115637},
pmid = {39967137},
issn = {1873-7145},
mesh = {*Listeria monocytogenes/growth & development/genetics/isolation & purification ; *Milk/microbiology ; Animals ; *Refrigeration ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; Cold Temperature ; },
abstract = {Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.},
}

*Listeria monocytogenes/growth & development/genetics/isolation & purification
*Milk/microbiology
Animals
*Refrigeration
*Microbiota
*Food Microbiology
RNA, Ribosomal, 16S/genetics
Food Contamination/analysis
Cold Temperature

@article {pmid39966419,
year = {2025},
author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N},
title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {30},
pmid = {39966419},
issn = {2055-5008},
mesh = {Animals ; Dogs ; *Dental Plaque/microbiology ; *Microbiota ; Humans ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; Phylogeny ; Pets/microbiology ; },
abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.},
}

Animals
Dogs
*Dental Plaque/microbiology
*Microbiota
Humans
Bacteria/classification/genetics/isolation & purification
Metagenome
Metagenomics/methods
Phylogeny
Pets/microbiology

@article {pmid39964655,
year = {2025},
author = {Pitt, A and Lienbacher, S and Schmidt, J and Neumann-Schaal, M and Wolf, J and Wenng, H and Oren, A and Huber, Z and Hahn, MW},
title = {Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39964655},
issn = {1618-1905},
abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.},
}

@article {pmid39962698,
year = {2025},
author = {Ye, Y and Guo, XW and Yang, MQ and Min, W and Guo, HJ},
title = {[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {2},
pages = {1225-1235},
doi = {10.13227/j.hjkx.202402036},
pmid = {39962698},
issn = {0250-3301},
mesh = {*Phosphorus/metabolism ; *Gossypium/growth & development/genetics ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Salinity ; Saline Waters ; Bacteria/genetics/classification/metabolism/growth & development ; },
abstract = {Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater （0.35 dS·m[-1], FW） and brackish water （8.04 dS·m[-1], SW）. The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content； electrical conductivity； quick phosphorus； and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes； and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3； organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW； transport genes phnK, phnE, phnC, and phnD； and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.},
}

*Phosphorus/metabolism
*Gossypium/growth & development/genetics
*Agricultural Irrigation/methods
*Soil Microbiology
*Soil/chemistry
Microbiota
Salinity
Saline Waters
Bacteria/genetics/classification/metabolism/growth & development

@article {pmid39929003,
year = {2025},
author = {Bakir-Gungor, B and Temiz, M and Canakcimaksutoglu, B and Yousef, M},
title = {Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach.},
journal = {Computers in biology and medicine},
volume = {187},
number = {},
pages = {109813},
doi = {10.1016/j.compbiomed.2025.109813},
pmid = {39929003},
issn = {1879-0534},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; *Biomarkers, Tumor/genetics ; Metagenomics/methods ; Algorithms ; Bacteria/genetics/classification ; },
abstract = {Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.},
}

*Colorectal Neoplasms/microbiology
Humans
*Gastrointestinal Microbiome/genetics
*Biomarkers, Tumor/genetics
Metagenomics/methods
Algorithms
Bacteria/genetics/classification

@article {pmid39880958,
year = {2025},
author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and , and Bhatt, AS and Hazelhurst, S},
title = {Expanding the human gut microbiome atlas of Africa.},
journal = {Nature},
volume = {638},
number = {8051},
pages = {718-728},
pmid = {39880958},
issn = {1476-4687},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenome ; Cross-Sectional Studies ; HIV Infections/microbiology/epidemiology ; Adult ; Treponema/isolation & purification/genetics/classification ; Africa ; Urban Population/statistics & numerical data ; Life Style ; Metagenomics ; South Africa/epidemiology ; Rural Population/statistics & numerical data ; Atlases as Topic ; Ghana ; },
abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.},
}

Humans
*Gastrointestinal Microbiome/genetics
Female
*Metagenome
Cross-Sectional Studies
HIV Infections/microbiology/epidemiology
Adult
Treponema/isolation & purification/genetics/classification
Africa
Urban Population/statistics & numerical data
Life Style
Metagenomics
South Africa/epidemiology
Rural Population/statistics & numerical data
Atlases as Topic
Ghana

@article {pmid39875062,
year = {2025},
author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y},
title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {272},
number = {},
pages = {110430},
doi = {10.1016/j.clim.2025.110430},
pmid = {39875062},
issn = {1521-7035},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/complications ; *Lung Diseases, Interstitial/immunology ; *COVID-19/immunology/complications ; Male ; Female ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/immunology ; *Indican ; *SARS-CoV-2 ; *Microbiota ; Neutrophils/immunology ; Lung/immunology ; Pneumonia/immunology/complications/microbiology ; },
abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.

METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.

RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.

CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.},
}

Humans
*Arthritis, Rheumatoid/immunology/complications
*Lung Diseases, Interstitial/immunology
*COVID-19/immunology/complications
Male
Female
Middle Aged
Aged
*Bronchoalveolar Lavage Fluid/immunology
*Indican
*SARS-CoV-2
*Microbiota
Neutrophils/immunology
Lung/immunology
Pneumonia/immunology/complications/microbiology

@article {pmid39840975,
year = {2025},
author = {Ge, B and McDonald, RC and Yang, Q and Domesle, KJ and Sarria, S and Li, X and Hsu, C-H and Jarvis, KG and Tadesse, DA},
title = {Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {2},
pages = {e0223024},
doi = {10.1128/aem.02230-24},
pmid = {39840975},
issn = {1098-5336},
mesh = {*RNA, Ribosomal, 16S/genetics ; Animals ; *Microbiota ; *Metagenomics ; *Animal Feed/analysis/microbiology ; Dogs ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Cattle ; Food Microbiology ; Drug Resistance, Bacterial/genetics ; Poultry/microbiology ; DNA, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Sequence Analysis, DNA ; },
abstract = {As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood & Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.},
}

*RNA, Ribosomal, 16S/genetics
Animals
*Microbiota
*Metagenomics
*Animal Feed/analysis/microbiology
Dogs
*Bacteria/genetics/isolation & purification/classification/drug effects
Cattle
Food Microbiology
Drug Resistance, Bacterial/genetics
Poultry/microbiology
DNA, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Sequence Analysis, DNA

@article {pmid39840973,
year = {2025},
author = {Wu, DG and Harris, CR and Kalis, KM and Bowen, M and Biddle, JF and Farag, IF},
title = {Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {2},
pages = {e0222924},
doi = {10.1128/aem.02229-24},
pmid = {39840973},
issn = {1098-5336},
support = {//Midlin Foundation/ ; //W. M. Keck Foundation (WMKF)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Metagenomics ; *Diet/veterinary ; *Fishes/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Animal Feed/analysis ; Coral Reefs ; Feces/microbiology ; },
abstract = {UNLABELLED: Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.

IMPORTANCE: The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.},
}

Animals
*Gastrointestinal Microbiome
*Metagenomics
*Diet/veterinary
*Fishes/microbiology
Bacteria/classification/genetics/isolation & purification
Metagenome
Animal Feed/analysis
Coral Reefs
Feces/microbiology