@article {pmid40053579,
year = {2025},
author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R},
title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.},
journal = {Science advances},
volume = {11},
number = {10},
pages = {eads5631},
doi = {10.1126/sciadv.ads5631},
pmid = {40053579},
issn = {2375-2548},
mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; },
abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.},
}

*Geologic Sediments/microbiology
*Deltaproteobacteria/metabolism/genetics
*Carbon Cycle
Sulfur/metabolism
Gene Regulatory Networks
Phylogeny
Metagenome
Carbon/metabolism
Proteome/metabolism
Oxidation-Reduction
Metabolic Networks and Pathways

@article {pmid40052474,
year = {2025},
author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M},
title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70156},
doi = {10.1111/1541-4337.70156},
pmid = {40052474},
issn = {1541-4337},
support = {//United Arab Emirates University/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; },
abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.},
}

*Gastrointestinal Microbiome/drug effects
*Nanoparticles/chemistry
*Polysaccharides/chemistry
*Functional Food
Humans
Plants/chemistry

@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.},
}

Humans
Male
*HIV Infections/complications/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Akkermansia
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Prospective Studies
Feces/microbiology
Metagenomics/methods
Hyperlipidemias/microbiology
Metabolic Diseases/microbiology/epidemiology
Verrucomicrobia/isolation & purification
Overweight/microbiology/complications

@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}

@article {pmid39726137,
year = {2025},
author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N},
title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14060},
doi = {10.1111/1755-0998.14060},
pmid = {39726137},
issn = {1755-0998},
support = {01UT2101C//Bundesministerium für Bildung und Forschung/ ; 01UT2101B//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; },
abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.},
}

*Biodiversity
Animals
*Amphibians/genetics/classification
*Ponds
Germany
*DNA Barcoding, Taxonomic/methods
*Lakes
Odonata/genetics/classification
Metagenomics/methods
DNA, Environmental/genetics
Aquatic Organisms/genetics/classification

@article {pmid40050382,
year = {2025},
author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q},
title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7910},
pmid = {40050382},
issn = {2045-2322},
support = {32230071//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; },
abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.},
}

Animals
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Coleoptera/microbiology/genetics
Metagenome
Bacteria/genetics/classification/metabolism
Microbiota
Symbiosis
Weevils/microbiology/genetics
Phylogeny

@article {pmid40049907,
year = {2025},
author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J},
title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {678-690},
doi = {10.1016/j.jes.2024.10.002},
pmid = {40049907},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; },
abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.},
}

*Soil Microbiology
*Mining
*Plant Development
*Soil/chemistry
Phosphorus/metabolism
Carbon/metabolism
Biodegradation, Environmental
Nitrogen/metabolism
Microbiota
Bacillus thuringiensis

@article {pmid40049896,
year = {2025},
author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H},
title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {550-562},
doi = {10.1016/j.jes.2024.08.026},
pmid = {40049896},
issn = {1001-0742},
mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; },
abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.},
}

*Bacteria/metabolism/classification/genetics
*Viruses
Phosphorus/analysis
RNA, Ribosomal, 16S/genetics
Nitrogen/analysis
Carbon/metabolism
Water Microbiology
Water Pollutants, Chemical/analysis
Nutrients/analysis

@article {pmid40047330,
year = {2025},
author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L},
title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.},
journal = {Journal of food science},
volume = {90},
number = {3},
pages = {e70106},
doi = {10.1111/1750-3841.70106},
pmid = {40047330},
issn = {1750-3841},
support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; },
abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colitis/chemically induced
*Dextran Sulfate
Mice
Male
Disease Models, Animal
Mice, Inbred C57BL
Colon/metabolism/microbiology/drug effects
Cytokines/metabolism
Intestines/microbiology/drug effects

@article {pmid39893934,
year = {2025},
author = {Zeng, S and Mo, S and Wu, X and Meng, C and Peng, P and Kashif, M and Li, J and He, S and Jiang, C},
title = {Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge.},
journal = {Marine environmental research},
volume = {205},
number = {},
pages = {106980},
doi = {10.1016/j.marenvres.2025.106980},
pmid = {39893934},
issn = {1879-0291},
mesh = {*Carbon/metabolism ; *Wetlands ; Animals ; Microbiota ; Aquaculture ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/genetics/classification ; Ponds/microbiology ; },
abstract = {Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.},
}

*Carbon/metabolism
*Wetlands
Animals
Microbiota
Aquaculture
Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/metabolism/genetics/classification
Ponds/microbiology

@article {pmid39708826,
year = {2025},
author = {Hu, Y and Zhang, ZY and Wang, F and Zhuang, K and Xu, X and Liu, DS and Fan, HZ and Yang, L and Jiang, K and Zhang, DK and Xu, L and Tang, JH and Liu, XM and He, C and Shu, X and Xie, Y and Lau, JYW and Zhu, Y and Du, YQ and Graham, DY and Lu, NH},
title = {Effects of amoxicillin dosage on cure rate, gut microbiota, and antibiotic resistome in vonoprazan and amoxicillin dual therapy for Helicobacter pylori: a multicentre, open-label, non-inferiority randomised controlled trial.},
journal = {The Lancet. Microbe},
volume = {6},
number = {3},
pages = {100975},
doi = {10.1016/j.lanmic.2024.100975},
pmid = {39708826},
issn = {2666-5247},
mesh = {Humans ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; Middle Aged ; Female ; Male ; *Amoxicillin/administration & dosage/pharmacology/therapeutic use ; *Sulfonamides/administration & dosage/pharmacology/therapeutic use/adverse effects ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Drug Therapy, Combination ; *Pyrroles/administration & dosage/pharmacology/therapeutic use ; *Anti-Bacterial Agents/administration & dosage/pharmacology/therapeutic use/adverse effects ; Aged ; Treatment Outcome ; Young Adult ; Adolescent ; Drug Resistance, Bacterial/genetics ; China ; Proton Pump Inhibitors/administration & dosage/pharmacology/therapeutic use/adverse effects ; },
abstract = {BACKGROUND: Vonoprazan and amoxicillin (VA) dual therapy as a mainstream Helicobacter pylori regimen has gained momentum worldwide, but the optimum dosages remain unclear. We aimed to compare the efficacy and safety of VA dual therapy with 2 g amoxicillin or 3 g amoxicillin, and to assess the short-term effects of therapy on the gut microbiota and antibiotic resistome.

METHODS: We conducted an open-label, non-inferiority randomised controlled trial at 12 centres in China. Individuals infected with H pylori, aged 18-70 years, and without previous eradication therapy were recruited. Participants were randomly assigned at a 1:1 ratio (block size of six) to receive vonoprazan (20 mg twice a day) with either low-dose amoxicillin (1 g twice a day; LVA therapy) or high-dose amoxicillin (1 g three times a day; HVA therapy) for 14 days. Gastric biopsies were collected before treatment for detection of antibiotic resistance. Stool samples were collected at baseline, week 2, and week 8-10 for shotgun metagenomic sequencing. The primary outcome was the eradication rate of H pylori, assessed by [13]C urea breath test, in both intention-to-treat and per-protocol analyses. Secondary outcomes were adverse events, adherence, antibiotic resistance, and alterations to the gut microbiota and antibiotic resistome. The margin used to establish non-inferiority was -0·10. The trial was registered with ClinicalTrials.gov, NCT05649709.

FINDINGS: Between Feb 13, 2023, and Jan 25, 2024, 504 patients (204 [40%] male and 300 [60%] female; mean age 43 years [SD 13]) were randomly assigned to LVA therapy or HVA therapy (n=252 in each group). No infections were resistant to amoxicillin. The H pylori eradication rate was 85·3% (215 of 252; 95% CI 80·4 to 89·2) in the LVA group and 86·5% (218 of 252; 81·7 to 90·2) in the HVA group in the intention-to-treat analysis (p=0·70) and 88·8% (213 of 240; 84·1 to 92·2) and 92·4% (218 of 236; 88·3 to 95·1), respectively, in the per-protocol analysis (p=0·18). The efficacy of LVA was non-inferior to HVA in the intention-to-treat analysis (risk difference -1·2%, 95% CI -7·3 to 4·9, p=0·0022) and the per-protocol analysis (-3·6%, -9·0 to 1·7, p=0·0085). 31 (12%) patients in the LVA group and 43 (17%) patients in the HVA group reported adverse events. Adherence to therapy was 97% in the LVA group and 96% in the HVA group. The diversity of gut microbiota decreased after treatment but was restored to baseline at week 8-10 in both groups. The abundance of beta-lactam-related resistance genes was increased at week 2 after treatment, and was restored to pretreatment level at week 8-10 for the LVA group but not the HVA group.

INTERPRETATION: LVA dual therapy was effective and non-inferior to HVA dual therapy as first-line treatment of H pylori infection and showed a non-lasting effect on the abundance of beta-lactam-related resistance genes. High amoxicillin dosage (eg, 3 g per day) is not required to achieve high cure rates with vonoprazan dual therapy.

FUNDING: National Natural Science Foundation of China, Project for Academic and Technical Leaders of Major Disciplines in Jiangxi Province, and Key Research and Development Program of Jiangxi Province.},
}

Humans
*Helicobacter Infections/drug therapy/microbiology
*Helicobacter pylori/drug effects/genetics
Middle Aged
Female
Male
*Amoxicillin/administration & dosage/pharmacology/therapeutic use
*Sulfonamides/administration & dosage/pharmacology/therapeutic use/adverse effects
Adult
*Gastrointestinal Microbiome/drug effects
*Drug Therapy, Combination
*Pyrroles/administration & dosage/pharmacology/therapeutic use
*Anti-Bacterial Agents/administration & dosage/pharmacology/therapeutic use/adverse effects
Aged
Treatment Outcome
Young Adult
Adolescent
Drug Resistance, Bacterial/genetics
China
Proton Pump Inhibitors/administration & dosage/pharmacology/therapeutic use/adverse effects

@article {pmid39653411,
year = {2025},
author = {Shi, Z and Li, M and Zhang, C and Li, H and Zhang, Y and Zhang, L and Li, X and Li, L and Wang, X and Fu, X and Sun, Z and Zhang, X and Tian, L and Zhang, M and Chen, WH and Li, Z},
title = {Butyrate-producing Faecalibacterium prausnitzii suppresses natural killer/T-cell lymphoma by dampening the JAK-STAT pathway.},
journal = {Gut},
volume = {74},
number = {4},
pages = {557-570},
doi = {10.1136/gutjnl-2024-333530},
pmid = {39653411},
issn = {1468-3288},
mesh = {Animals ; Humans ; Mice ; *Gastrointestinal Microbiome/physiology ; *Faecalibacterium prausnitzii/metabolism ; *Butyrates/metabolism ; Janus Kinases/metabolism ; Cross-Sectional Studies ; Female ; Male ; STAT Transcription Factors/metabolism ; Signal Transduction ; Lymphoma, Extranodal NK-T-Cell/metabolism/microbiology/pathology ; Probiotics/therapeutic use ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive malignancy with a dismal prognosis, and gaps remain in understanding the determinants influencing disease outcomes.

OBJECTIVE: To characterise the gut microbiota feature and identify potential probiotics that could ameliorate the development of NKTCL.

DESIGN: This cross-sectional study employed shotgun metagenomic sequencing to profile the gut microbiota in two Chinese NKTCL cohorts, with validation conducted in an independent Korean cohort. Univariable and multivariable Cox proportional hazards analyses were applied to assess associations between identified marker species and patient outcomes. Tumour-suppressing effects were investigated using comprehensive in vivo and in vitro models. In addition, metabolomics, RNA sequencing, chromatin immunoprecipitation sequencing, Western blot analysis, immunohistochemistry and lentiviral-mediated gene knockdown system were used to elucidate the underlying mechanisms.

RESULTS: We first unveiled significant gut microbiota dysbiosis in NKTCL patients, prominently marked by a notable reduction in Faecalibacterium prausnitzii which correlated strongly with shorter survival among patients. Subsequently, we substantiated the antitumour properties of F. prausnitzii in NKTCL mouse models. Furthermore, F. prausnitzii culture supernatant demonstrated significant efficacy in inhibiting NKTCL cell growth. Metabolomics analysis revealed butyrate as a critical metabolite underlying these tumour-suppressing effects, validated in three human NKTCL cell lines and multiple tumour-bearing mouse models. Mechanistically, butyrate suppressed the activation of Janus kinase-signal transducer and activator of transcription pathway through enhancing histone acetylation, promoting the expression of suppressor of cytokine signalling 1.

CONCLUSION: These findings uncover a distinctive gut microbiota profile in NKTCL and provide a novel perspective on leveraging the therapeutic potential of F. prausnitzii to ameliorate this malignancy.},
}

Animals
Humans
Mice
*Gastrointestinal Microbiome/physiology
*Faecalibacterium prausnitzii/metabolism
*Butyrates/metabolism
Janus Kinases/metabolism
Cross-Sectional Studies
Female
Male
STAT Transcription Factors/metabolism
Signal Transduction
Lymphoma, Extranodal NK-T-Cell/metabolism/microbiology/pathology
Probiotics/therapeutic use
Dysbiosis/microbiology
Middle Aged

@article {pmid38508446,
year = {2025},
author = {Tao, S and Fan, J and Li, J and Wu, Z and Yao, Y and Wang, Z and Wu, Y and Liu, X and Xiao, Y and Wei, H},
title = {Extracellular vesicles derived from Lactobacillus johnsonii promote gut barrier homeostasis by enhancing M2 macrophage polarization.},
journal = {Journal of advanced research},
volume = {69},
number = {},
pages = {545-563},
doi = {10.1016/j.jare.2024.03.011},
pmid = {38508446},
issn = {2090-1224},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Extracellular Vesicles/metabolism ; Mice ; *Macrophages/metabolism/immunology/microbiology ; Swine ; *Diarrhea/microbiology/therapy ; *Probiotics ; *Lactobacillus johnsonii/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Homeostasis ; Fecal Microbiota Transplantation/methods ; Macrophage Activation ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {INTRODUCTION: Diarrheic disease is a common intestinal health problem worldwide, causing great suffering to humans and animals. Precise manipulation strategies based on probiotics to combat diarrheic diseases have not been fully developed.

OBJECTIVES: The aim of this study was to investigate the molecular mechanisms by which probiotics manipulate macrophage against diarrheic disease.

METHODS: Metagenome reveals gut microbiome profiles of healthy and diarrheic piglets. Fecal microbial transplantation (FMT) was employed to explore the causal relationship between gut microbes and diarrhea. The protective role of probiotics and their derived extracellular vesicles (EVs) was investigated in ETEC K88-infected mice. Macrophage depletion was performed to assess the role of macrophages in EVs against diarrhea. Execution of in vitro cell co-culture and transcriptome analyses elucidated the molecular mechanisms by which EVs modulate the macrophage and intestinal epithelial barrier.

RESULTS: Escherichia coli was enriched in weaned diarrheic piglets, while Lactobacillus johnsonii (L. john) showed a negative correlation with Escherichia coli. The transmission of diarrheic illness symptoms was achieved by transferring fecal microbiota, but not metabolites, from diarrheic pigs to germ-free (GF) mice. L. john's intervention prevented the transmission of disease phenotypes from diarrheic piglets to GF mice. L. john also reduces the gut inflammation induced by ETEC K88. The EVs secreted by L. john demonstrated enhanced efficacy in mitigating the adverse impacts induced by ETEC K88 through the modulation of macrophage phenotype. In vitro experiments have revealed that EVs activate M2 macrophages in a manner that shuts down ERK, thereby inhibiting NLRP3 activation in intestinal epithelial cells.

CONCLUSION: Our results reveal that intestinal microbiota drives the onset of diarrheic disease and that probiotic-derived EVs ameliorate diarrheic disease symptoms by modulating macrophage phenotypes. These findings can enhance the advancement of innovative therapeutic approaches for diarrheic conditions based on probiotic-derived EVs.},
}

Animals
*Gastrointestinal Microbiome
*Extracellular Vesicles/metabolism
Mice
*Macrophages/metabolism/immunology/microbiology
Swine
*Diarrhea/microbiology/therapy
*Probiotics
*Lactobacillus johnsonii/metabolism
Intestinal Mucosa/microbiology/metabolism
Homeostasis
Fecal Microbiota Transplantation/methods
Macrophage Activation
Humans
Mice, Inbred C57BL
Feces/microbiology

@article {pmid40045185,
year = {2025},
author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL},
title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {120},
pmid = {40045185},
issn = {1471-2180},
support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; },
mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; },
abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.},
}

California
*Sulfur/metabolism
*Microbiota
*Lakes/microbiology
*Seawater/microbiology/chemistry
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seasons
Phylogeny
RNA, Ribosomal, 16S/genetics
Ecosystem
Biodiversity

@article {pmid40044917,
year = {2025},
author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A},
title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.},
journal = {Mycorrhiza},
volume = {35},
number = {2},
pages = {17},
pmid = {40044917},
issn = {1432-1890},
support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.},
}

*Mycorrhizae/physiology
*Vitis/microbiology
*Soil Microbiology
*Soil/chemistry
Czech Republic
Plant Roots/microbiology
Mycobiome
Basidiomycota/genetics/physiology
Rhizosphere
Phosphorus/metabolism/analysis

@article {pmid40044690,
year = {2025},
author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M},
title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2226},
pmid = {40044690},
issn = {2041-1723},
support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; },
abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .},
}

*RNA, Viral/genetics
*RNA Viruses/genetics/classification/isolation & purification
*DNA Viruses/genetics/classification
*DNA, Viral/genetics
Software
Phylogeny
Genome, Viral/genetics
Metagenomics/methods
Virome/genetics
Computational Biology/methods

@article {pmid40044673,
year = {2025},
author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G},
title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1798},
pmid = {40044673},
issn = {2041-1723},
mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; },
abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.},
}

Animals
Antarctic Regions
*Spheniscidae/genetics
*DNA, Mitochondrial/genetics
*Geologic Sediments
Phylogeny
Seals, Earless
Metagenome
Ecosystem
Diet

@article {pmid40043057,
year = {2025},
author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI},
title = {What defines a photosynthetic microbial mat in western Antarctica?.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315919},
doi = {10.1371/journal.pone.0315919},
pmid = {40043057},
issn = {1932-6203},
mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation & purification ; Photosynthesis ; Archaea/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; Microbiota ; },
abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.},
}

Antarctic Regions
*Bacteria/genetics/classification/isolation & purification
Photosynthesis
Archaea/genetics/classification/isolation & purification
Biodiversity
Phylogeny
Microbiota

@article {pmid40042126,
year = {2025},
author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB},
title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.},
journal = {Pediatric pulmonology},
volume = {60},
number = {3},
pages = {e71024},
doi = {10.1002/ppul.71024},
pmid = {40042126},
issn = {1099-0496},
support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; },
mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; },
abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

CONCLUSIONS: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.},
}

Humans
*Cystic Fibrosis/microbiology/drug therapy
*Feces/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Infant
*Oropharynx/microbiology
Male
Female
*Microbiota/drug effects
beta-Lactams/pharmacology/therapeutic use
Bacterial Load/drug effects
Longitudinal Studies

@article {pmid40040342,
year = {2025},
author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J},
title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70047},
doi = {10.1002/ecy.70047},
pmid = {40040342},
issn = {1939-9170},
support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.},
}

*Lakes/microbiology
*Adaptation, Physiological
*Bacteria/classification/genetics
Bacterial Physiological Phenomena
Microbiota
Hydrogen-Ion Concentration

@article {pmid40038838,
year = {2025},
author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K},
title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {65},
pmid = {40038838},
issn = {2049-2618},
support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; },
mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; },
abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.},
}

Humans
*Skin/microbiology
*Microbiota/genetics
*DNA, Bacterial/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Bacterial Load
Healthy Volunteers
Adult
Female
Male

@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; },
mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}

China
*Microbiota
*Archaea/genetics
*Bacteria/genetics/classification
*Bays
Seawater/microbiology
Metagenome
Multiomics

@article {pmid40038282,
year = {2025},
author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL},
title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2186},
pmid = {40038282},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; },
mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; },
abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.},
}

*Ecosystem
*Methane/metabolism
*Genomics/methods
*Microbiota/genetics
Arctic Regions
Metagenomics/methods
Wetlands
Greenhouse Gases/metabolism
Climate Change
Bacteria/genetics/metabolism/classification

@article {pmid40038255,
year = {2025},
author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F},
title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {79},
pmid = {40038255},
issn = {2059-3635},
support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; },
abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.},
}

*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism
Animals
Mice
*Gastrointestinal Microbiome
Humans
*Dysbiosis/genetics/microbiology/metabolism
Female
*beta Catenin/genetics/metabolism
*Stress, Psychological/genetics/microbiology/metabolism
Neoplastic Stem Cells/metabolism/pathology
Wnt Signaling Pathway/genetics
Breast Neoplasms/genetics/metabolism/pathology/microbiology

@article {pmid40037564,
year = {2025},
author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB},
title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.},
journal = {Age and ageing},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/ageing/afaf042},
pmid = {40037564},
issn = {1468-2834},
support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; },
mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation & purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics & numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics & numerical data ; Age Factors ; Long-Term Care/statistics & numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; },
abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.},
}

Humans
Male
Female
*Staphylococcal Infections/mortality/microbiology/diagnosis
Aged, 80 and over
Aged
*Staphylococcus aureus/isolation & purification
*Oropharynx/microbiology
*Homes for the Aged/statistics & numerical data
Risk Factors
South Australia/epidemiology
Nursing Homes/statistics & numerical data
Age Factors
Long-Term Care/statistics & numerical data
Carrier State/microbiology/diagnosis
Time Factors
Metagenomics
Microbiota
Comorbidity
Cause of Death
Risk Assessment
Methicillin-Resistant Staphylococcus aureus/isolation & purification

@article {pmid40036691,
year = {2025},
author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX},
title = {Benchmarking short-read metagenomics tools for removing host contamination.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40036691},
issn = {2047-217X},
support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; },
abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.

RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.

CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.},
}

*Metagenomics/methods
*Benchmarking
Microbiota/genetics
Humans
DNA Contamination
Metagenome
Software
Sequence Analysis, DNA/methods
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Reproducibility of Results

@article {pmid40032396,
year = {2025},
author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA},
title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e092938},
pmid = {40032396},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; },
abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.

METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3 months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.

ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.

TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.},
}

Humans
*Gastrointestinal Microbiome
Switzerland
Infant
Infant, Newborn
*Sleep/physiology
Double-Blind Method
Child Development
Infant, Premature
Child, Preschool
Brain-Gut Axis
Female
Randomized Controlled Trials as Topic
Male
Probiotics/therapeutic use
Multicenter Studies as Topic

@article {pmid40030030,
year = {2025},
author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK},
title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2413953122},
doi = {10.1073/pnas.2413953122},
pmid = {40030030},
issn = {1091-6490},
support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation & purification ; Mice, Inbred C57BL ; Case-Control Studies ; },
abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.},
}

*Gastrointestinal Microbiome
*Multiple Sclerosis/microbiology
Animals
Humans
Mice
Female
*Dysbiosis/microbiology
*Feces/microbiology
Male
Akkermansia
Adult
Encephalomyelitis, Autoimmune, Experimental/microbiology
Middle Aged
Bifidobacterium
Prevotella/isolation & purification
Mice, Inbred C57BL
Case-Control Studies

@article {pmid40028749,
year = {2025},
author = {Salahi, A and Abd El-Ghany, WA},
title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70263},
pmid = {40028749},
issn = {2053-1095},
mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; },
abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.},
}

Animals
*Archaea/physiology
Humans
*Poultry
Livestock
Gastrointestinal Microbiome

@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 = {273},
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 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 {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 {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 {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 {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 {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 {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 {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 = {},
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 = {},
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 = {},
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 = {},
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 = {},
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 = {},
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 = {},
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 = {},
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 {pmid39999861,
year = {2025},
author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD},
title = {Rhizosphere microbiome influence on tomato growth under low-nutrient settings.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {3},
pages = {},
pmid = {39999861},
issn = {1574-6941},
support = {DGAPA-PAPIIT-UNAM IN206824//Universidad Nacional Autónoma de México/ ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/growth & development/isolation & purification ; *Plant Roots/microbiology/growth & development ; Nutrients/metabolism ; Metagenomics ; Hydroponics ; Biomass ; },
abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.},
}

*Solanum lycopersicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/growth & development/isolation & purification
*Plant Roots/microbiology/growth & development
Nutrients/metabolism
Metagenomics
Hydroponics
Biomass

@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 = {},
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 {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 = {},
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 {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},
mesh = {Brazil ; *Rivers/microbiology/chemistry ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Metals/analysis ; },
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.},
}

Brazil
*Rivers/microbiology/chemistry
*Environmental Monitoring
*Water Pollutants, Chemical/analysis
*Drug Resistance, Microbial/genetics
Metals/analysis

@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 {pmid39983489,
year = {2025},
author = {Karlsson, M and Jönsson, HL and Hultberg, M},
title = {Inclusion of biochar in mushroom substrate influences microbial community composition of the substrate and elemental composition of the fruiting bodies.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178914},
doi = {10.1016/j.scitotenv.2025.178914},
pmid = {39983489},
issn = {1879-1026},
mesh = {*Charcoal/chemistry ; *Fruiting Bodies, Fungal/chemistry ; *Microbiota ; Soil Microbiology ; Pleurotus ; Agaricales/chemistry ; Soil/chemistry ; Bacteria/classification ; },
abstract = {Due to its structure, biochar makes the soil porous and oxygen-rich, enhancing the water-holding capacity and increasing the cation exchange capacity for a longer duration. These aspects could also be favourable for mushroom production. However, biochar has been considerably less investigated within this context. This study investigated the impact of biochar on mushroom production, quality, and the microbial communities of the substrates. Two different biochar's produced from local feedstocks, plant- or sludge based, were evaluated in the production of oyster mushrooms (Pleurotus ostreatus) at two different concentrations (5 % and 10 %). The results showed that inclusion of biochar in the substrate negatively impacted fruiting body production. The elemental composition of the fruiting body was also affected by inclusion of biochar and partly reflected the elemental composition of the biochar. The metagenomics revealed that inclusion of biochar in the substrate altered the microbial community structure. The bacterial diversity based on Shannon indices was higher in the substrate wherein no biochar was added. Bacterial community richness (Chao 1) was higher in samples with biochar compared to the control with no added biochar. Fungal community richness based on Chao 1 indices displayed an increase in samples with an inclusion of biochar. Overall, this study provides novel insights into the impact of biochar in mushroom production regarding its concentration and the effect of the origin material of the biochar.},
}

*Charcoal/chemistry
*Fruiting Bodies, Fungal/chemistry
*Microbiota
Soil Microbiology
Pleurotus
Agaricales/chemistry
Soil/chemistry
Bacteria/classification

@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 {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 {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 {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 = {},
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 {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 {pmid39958933,
year = {2025},
author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P},
title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1511625},
pmid = {39958933},
issn = {2235-2988},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; },
abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.

METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.

RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.

DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.},
}

Humans
Female
*Endometrial Neoplasms/microbiology/genetics
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Uterus/microbiology
Middle Aged
Phylogeny
Biomarkers
Adult
Aged
Reactive Oxygen Species/metabolism
Carcinogenesis
Fibroblasts/microbiology
Biomarkers, Tumor/genetics
Computational Biology/methods
Oxidative Stress

@article {pmid39956110,
year = {2025},
author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU},
title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70056},
pmid = {39956110},
issn = {1462-2920},
support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; },
abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Bioreactors/microbiology
*Sulfides/metabolism
Sweden
*Nitrogen/metabolism
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Archaea/metabolism/genetics/classification
Seawater/microbiology
Bacteria/classification/genetics/metabolism
Oxidation-Reduction
Denitrification
Nitrates/metabolism
Phylogeny
Ecosystem

@article {pmid39955324,
year = {2025},
author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO},
title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5619},
pmid = {39955324},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation & purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; },
abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.},
}

Humans
*Gastrointestinal Microbiome/genetics
Male
Adult
*Athletes
Female
*Feces/microbiology
Metagenomics/methods
Prevotella/genetics/isolation & purification
Young Adult
Running
Faecalibacterium prausnitzii/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 {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 {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},
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 {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}

*Metagenomics
*Vegetables/virology/microbiology
*Fermentation
*Bacteriophages/genetics/isolation & purification/classification
Microbiota
Brassica/microbiology/virology
Fermented Foods/microbiology/virology
Bacteria/genetics/classification/isolation & purification/virology
Biodiversity
Daucus carota/microbiology/virology
Food Microbiology
Viruses/isolation & purification/classification/genetics
Enterobacteriaceae/isolation & purification/genetics/virology/classification
Metagenome
Lactobacillaceae/isolation & purification/genetics/classification

@article {pmid39952762,
year = {2025},
author = {Li, Z and Liao, Y and Huang, C and Liu, J and Kong, X and Li, L and Li, Z and Gui, Y},
title = {Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104718},
doi = {10.1016/j.fm.2024.104718},
pmid = {39952762},
issn = {1095-9998},
mesh = {*Fermentation ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Flavoring Agents/metabolism/chemistry ; *Fungi/classification/metabolism/genetics/isolation & purification ; China ; Gas Chromatography-Mass Spectrometry ; Amino Acids/metabolism/analysis ; Solid Phase Microextraction ; Food Microbiology ; Mycobiome ; Chromatography, High Pressure Liquid ; Condiments/microbiology/analysis ; },
abstract = {Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.},
}

*Fermentation
*Acetic Acid/metabolism/analysis
*Volatile Organic Compounds/metabolism/analysis/chemistry
*Flavoring Agents/metabolism/chemistry
*Fungi/classification/metabolism/genetics/isolation & purification
China
Gas Chromatography-Mass Spectrometry
Amino Acids/metabolism/analysis
Solid Phase Microextraction
Food Microbiology
Mycobiome
Chromatography, High Pressure Liquid
Condiments/microbiology/analysis

@article {pmid39952751,
year = {2025},
author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F},
title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104734},
doi = {10.1016/j.fm.2025.104734},
pmid = {39952751},
issn = {1095-9998},
mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; },
abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.},
}

Animals
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Chickens/microbiology
*Food Storage
Poultry Products/microbiology
Food Packaging/methods
Food Microbiology
Poultry/microbiology
Drug Resistance, Bacterial
Temperature
Meat/microbiology
Brochothrix/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Environmental Microbiology
Metagenomics

@article {pmid39951448,
year = {2025},
author = {Li, Q and Wu, X and Niu, X and Yu, Z and Fang, S and Chu, X and Zhu, J and Song, Q and Hou, C and Wei, X},
title = {Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0317832},
pmid = {39951448},
issn = {1932-6203},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Female ; *Ovariectomy ; *Osteoporosis/drug therapy/metabolism ; *Metabolomics ; Rats ; *Flavonoids/pharmacology ; *Bone Density/drug effects ; *Polypodiaceae ; Metagenomics ; Rats, Sprague-Dawley ; Drugs, Chinese Herbal/pharmacology ; Rhizome ; },
abstract = {TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Female
*Ovariectomy
*Osteoporosis/drug therapy/metabolism
*Metabolomics
Rats
*Flavonoids/pharmacology
*Bone Density/drug effects
*Polypodiaceae
Metagenomics
Rats, Sprague-Dawley
Drugs, Chinese Herbal/pharmacology
Rhizome

@article {pmid39951402,
year = {2025},
author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M},
title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0306503},
pmid = {39951402},
issn = {1932-6203},
support = {P20 GM103451/GM/NIGMS NIH HHS/United States ; P20 RR016480/RR/NCRR NIH HHS/United States ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; },
abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Biodegradation, Environmental
*Groundwater/microbiology
*Metagenome
*Tetrachloroethylene/metabolism
Water Pollutants, Chemical/metabolism
Halogenation
Metagenomics/methods
Bacteria/genetics/metabolism/classification
New Mexico

@article {pmid39951352,
year = {2025},
author = {Li, Q and Tan, D and Xiong, S and Yu, K and Su, Y and Zhu, W},
title = {Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2467185},
pmid = {39951352},
issn = {1949-0984},
mesh = {Animals ; *Glucagon-Like Peptide 1/metabolism/blood ; *Gastrointestinal Microbiome ; Swine ; *Tryptophan/metabolism ; *Lactobacillus/metabolism ; *Appetite/physiology ; Enteroendocrine Cells/metabolism ; Feeding Behavior ; Hypothalamus/metabolism ; },
abstract = {Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.},
}

Animals
*Glucagon-Like Peptide 1/metabolism/blood
*Gastrointestinal Microbiome
Swine
*Tryptophan/metabolism
*Lactobacillus/metabolism
*Appetite/physiology
Enteroendocrine Cells/metabolism
Feeding Behavior
Hypothalamus/metabolism

@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},
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 {pmid39950834,
year = {2025},
author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS},
title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {3},
pages = {e70023},
pmid = {39950834},
issn = {1478-3231},
support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; },
abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.

METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.

RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).

CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Glucosides/therapeutic use
Middle Aged
Prospective Studies
*Benzhydryl Compounds/therapeutic use
Non-alcoholic Fatty Liver Disease/drug therapy/microbiology
Treatment Outcome
Magnetic Resonance Imaging
Feces/microbiology
Sodium-Glucose Transporter 2 Inhibitors/therapeutic use
Logistic Models

@article {pmid39948426,
year = {2025},
author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X},
title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5400},
pmid = {39948426},
issn = {2045-2322},
support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; },
abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.},
}

Humans
Male
*Microbiota
Female
*Mouth/microbiology
*Saliva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Child
Goldenhar Syndrome/microbiology
Dysbiosis/microbiology
Adolescent
Adult
Bacteria/classification/genetics/isolation & purification/metabolism
Young Adult
Metagenomics/methods
Child, Preschool
Case-Control Studies

@article {pmid39948184,
year = {2025},
author = {Chen, A and Yu, Q and Zheng, L and Yi, J and Tang, Z and Ge, H and Ning, Y and Yin, N and Xie, Y and Chen, S and Shi, W and She, X and Xiang, J and Tang, J},
title = {Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {11},
pmid = {39948184},
issn = {1432-1831},
support = {81972198, 81773147//National Natural Science Foundation of China/ ; 2019SK2253//Key Research and Development Program of Hunan Province of China/ ; ZLXD2017004//Central South University/ ; ZLXD2017004//Central South University/ ; kq2208299//National Natural Science Foundation of Changsha/ ; },
mesh = {*Talaromyces ; Humans ; Animals ; *Macrophages/microbiology/immunology ; *Lung Neoplasms/microbiology ; Mice ; *Arginine/metabolism ; *Ornithine/metabolism/analogs & derivatives/pharmacology ; Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; Cell Proliferation ; Macrophage Activation ; Female ; Male ; Metagenomics ; Disease Models, Animal ; Cell Line, Tumor ; Mycobiome ; Lung/microbiology/pathology ; },
abstract = {It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.},
}

*Talaromyces
Humans
Animals
*Macrophages/microbiology/immunology
*Lung Neoplasms/microbiology
Mice
*Arginine/metabolism
*Ornithine/metabolism/analogs & derivatives/pharmacology
Carcinoma, Non-Small-Cell Lung/microbiology/pathology
Cell Proliferation
Macrophage Activation
Female
Male
Metagenomics
Disease Models, Animal
Cell Line, Tumor
Mycobiome
Lung/microbiology/pathology