@article {pmid41684896,
year = {2025},
author = {Das, R and Malard, L and Pearce, DA and Convey, P and Rahlff, J},
title = {Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726848},
pmid = {41684896},
issn = {1664-302X},
abstract = {Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their role in shaping ecosystems through microbial and nutrient interactions. We analyzed airborne viral community composition at two sites in South Georgia. Sampling took place using multiple methodologies, with the data produced subjected to viral metagenomics. The Coriolis μ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were only obtained from the coastal location, indicating that location influences airborne viral diversity. Protein-based clustering of 39 viral operational taxonomic units (vOTUs) revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the airborne viral community. Protein homologs related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed across major oceans, suggesting their potential role in supporting the resilience of marine microorganisms under changing climate conditions. Some vOTUs had protein similarities to viruses infecting extremophiles, indicating viral adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems. It underscores the need for continued monitoring to assess how these communities respond to shifting atmospheric and ecological conditions.},
}

@article {pmid41684743,
year = {2025},
author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL},
title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1729196},
pmid = {41684743},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Biofilms/growth & development ; Male ; Middle Aged ; Female ; Hispanic or Latino ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Chile ; Microbiota/genetics ; Metagenomics ; DNA, Bacterial/genetics ; Adult ; Bone and Bones/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics ; White ; },
abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.

METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the total bacterial community and the ribosomally active fraction. In three patients, samples were stratified by bone depth (superficial/top, middle and bottom). Microbial diversity and relative abundance were assessed across patients and bone layers.

RESULTS: Acute osteomyelitis was the predominant histopathological pattern. Culture yielded 19 bacterial isolates, 95% of which were Gram-negative bacilli. Sequencing identified 3,412 operational taxonomic units (OTUs), with Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Enterobacteriaceae and Enterococcaceae were the most ribosomally active families. Microbial community composition varied substantially among patients and across bone depths. Staphylococcus aureus was infrequent (5% of culture isolates; ~1% of sequence reads), whereas low-abundance but ribosomally active taxa, such as Corynebacteriaceae, were consistently detected across all layers.

DISCUSSION: This combined metagenomic and ribosomal transcript analysis reveals a polymicrobial, patient-specific bone microbiota in Chilean patients with DFO, highlighting potentially active bacteria frequently overlooked by standard diagnostic methods. These findings underscore the value of integrating molecular approaches into clinical workflows to improve pathogen detection and support more personalized antimicrobial strategies, while also helping to address gaps in microbiome research among underrepresented populations.},
}

Humans
*Diabetic Foot/microbiology/complications
*Osteomyelitis/microbiology
RNA, Ribosomal, 16S/genetics
*Biofilms/growth & development
Male
Middle Aged
Female
Hispanic or Latino
*Bacteria/classification/genetics/isolation & purification
Aged
Chile
Microbiota/genetics
Metagenomics
DNA, Bacterial/genetics
Adult
Bone and Bones/microbiology
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
DNA, Ribosomal/genetics
White

@article {pmid41684459,
year = {2026},
author = {Sgarabotto, E and Zadra, N and Tyrell, JA and Rossi, C and Hewson, I and Searle, JB and Hauffe, HC},
title = {Virome analysis reveals ORF7 sequences of type 2 porcine respiratory and reproductive syndrome virus (PRRSV) for the first time in a rodent host (Microtus pennsylvanicus).},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101345},
pmid = {41684459},
issn = {2352-7714},
abstract = {The lung virome of meadow vole (Microtus pennsylvanicus) from six neighbouring locations in New York State, USA was investigated using metagenomics to determine the circulation of potentially zoonotic viruses in a common wild rodent. This study provides the first evidence of the occurrence of Type 2 Porcine Respiratory and Reproductive Syndrome Virus (PRRSV2) in a rodent, or indeed in any species apart from wild and domestic pigs (Sus scrofa). PRRSV has the highest economic impact on the pig husbandry industry of any pathogen, but up to now, farm-to-farm transmission of this virus has been assumed to be associated with movement of and contact with infected pigs and fomites. Our results showing the natural occurrence of this virus in potential transmission hosts other than wild or domestic pigs challenge this scenario. Phylogenetic analysis of assembled partial genomes from four of our pooled samples and all other nucleocapsid protein (ORF7) sequences available in Genbank showed that the sequences recovered from meadow voles unambiguously clustered within the PRRSV2 clade together with sequences derived from wild and domestic pigs. Historical research suggests that spillover from voles to domestic pigs may be the most parsimonious explanation for these results; however, we cannot rule out the reverse: that the source of PRRSV2 in these wild voles derives from pigs. From a One Health perspective, our results reinforce the importance of characterizing wildlife viromes to survey possible sources of zoonotic pathogens, which is vital for making evidence-based decisions regarding potential threats to the health of humans, livestock and wild fauna.},
}

@article {pmid41588069,
year = {2026},
author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C},
title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6232},
pmid = {41588069},
issn = {2045-2322},
support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; },
mesh = {*Permafrost/microbiology ; *Caves/microbiology ; *Biomineralization ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; Phylogeny ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.},
}

*Permafrost/microbiology
*Caves/microbiology
*Biomineralization
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/metabolism
Phylogeny
*Microbiota
RNA, Ribosomal, 18S/genetics

@article {pmid41581442,
year = {2026},
author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W},
title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.},
journal = {Virology},
volume = {617},
number = {},
pages = {110814},
doi = {10.1016/j.virol.2026.110814},
pmid = {41581442},
issn = {1096-0341},
mesh = {Animals ; *Metagenomics ; *Animals, Wild/virology ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; Feces/virology ; Tibet ; *Virome ; Genome, Viral ; Genetic Variation ; Mammals/virology ; RNA, Viral/genetics ; },
abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.},
}

Animals
*Metagenomics
*Animals, Wild/virology
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
Feces/virology
Tibet
*Virome
Genome, Viral
Genetic Variation
Mammals/virology
RNA, Viral/genetics

@article {pmid41448339,
year = {2026},
author = {Ghosh, S and Ganguly, A and Dong, TS and Lagishetty, V and Jacobs, JP and Devaskar, SU},
title = {Intestinal microbiome in response to air pollutant exposure in pregestational and gestational murine females and their male and female offspring.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {140},
number = {},
pages = {109150},
doi = {10.1016/j.reprotox.2025.109150},
pmid = {41448339},
issn = {1873-1708},
mesh = {Female ; Animals ; Male ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Prenatal Exposure Delayed Effects/microbiology ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Mice ; Maternal Exposure ; Bacteria/genetics/drug effects/classification ; },
abstract = {We investigated the impact of chronic air pollutant (AP) exposure upon intestinal microbial diversity, composition, and metagenomic inferred functional pathways in murine pregestational and late gestational adult females, and male and female postnatal offspring (P21), compared to age- and sex- matched controls (CON). Intestinal microbiome analysis was undertaken with certain phenotypic characteristics in adult non-pregnant and pregnant females and the male and female offspring. In response to AP, pooled male and female offspring displayed no difference in E19 fetal and P1 postnatal body weights. At P21, females exposed in-utero to AP were heavier with increased fat and muscle mass at one month versus CON. Males were no different at P21 and 1 month revealing decreased fat mass and hyperglycemia. In pregestational/gestational females, AP did not change microbial α- or β-diversity from the respective CON. Gestational females showed AP induced changes in taxonomic composition such as reduced Bacteroides and increased Firmicutes, Verrucomicrobia, and Akkermansia, among others. In response to intra-uterine AP exposure, the offspring intestinal microbiome revealed more compelling differences in α- and β- diversity than adult females. While certain microbial changes were common in both sexes, sex-specific differences also emerged with reduced α-diversity, decreased Bacteroides and increased Akkermansia in males only. The metagenomic inferred pathways revealed perturbations in multiple pathways. We conclude that the offspring exposed in-utero to AP revealed sex-specific changes in microbial diversity, composition and function, displaying certain similarities with distinct differences from mothers. These early life changes were associated with the subsequent emergence of pre-diabetes and adiposity.},
}

Female
Animals
Male
Pregnancy
*Gastrointestinal Microbiome/drug effects
*Prenatal Exposure Delayed Effects/microbiology
*Air Pollutants/toxicity
Mice, Inbred C57BL
Mice
Maternal Exposure
Bacteria/genetics/drug effects/classification

@article {pmid41435895,
year = {2026},
author = {Zhang, PP and Cui, MY and Yang, SY and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF},
title = {Astragalus membranaceus improves blood glucose and renal function in diabetic kidney disease mice via gut microbial metabolite axis.},
journal = {Fitoterapia},
volume = {189},
number = {},
pages = {107048},
doi = {10.1016/j.fitote.2025.107048},
pmid = {41435895},
issn = {1873-6971},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Astragalus propinquus/chemistry ; Mice ; *Diabetic Nephropathies/drug therapy ; Male ; *Plant Extracts/pharmacology ; *Kidney/drug effects ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/drug therapy ; },
abstract = {Recent studies have demonstrated the therapeutic potential of Astragalus membranaceus in diabetic kidney disease (DKD); however, the underlying mechanisms remain incompletely elucidated. In this study, we established a streptozotocin-induced DKD mouse model to evaluate the effects of A. membranaceus extract (AME) on glycemic control, renal function, gut microbiota composition, and metabolic profiles. Biochemical analyzes revealed that A. membranaceus significantly attenuated hyperglycemia and improved renal function, as indicated by reduced serum creatinine and blood urea nitrogen levels. Metagenomic sequencing demonstrated that A. membranaceus reversed microbial dysbiosis by suppressing pathogenic bacteria (e.g., Aerococcus urinaeequi) and enriching beneficial probiotics (e.g., Thomasclavelia cocleata). Furthermore, LC/MS-based metabolomics identified key metabolic pathways, including glycerophospholipid metabolism and bile acid synthesis, as potential mediators of the therapeutic effects. These findings underscore the crucial role of the gut-renal axis in DKD pathogenesis and provide a mechanistic basis for the clinical application of A. membranaceus.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Astragalus propinquus/chemistry
Mice
*Diabetic Nephropathies/drug therapy
Male
*Plant Extracts/pharmacology
*Kidney/drug effects
*Blood Glucose/drug effects
Mice, Inbred C57BL
Diabetes Mellitus, Experimental/drug therapy

@article {pmid41683346,
year = {2026},
author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH},
title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/nu18030524},
pmid = {41683346},
issn = {2072-6643},
mesh = {Humans ; Pilot Projects ; Male ; Adult ; Female ; *Dietary Supplements ; Double-Blind Method ; *Exercise/physiology ; *Respiratory Tract Infections/prevention & control/immunology/epidemiology ; Gastrointestinal Microbiome/drug effects ; *Stress, Physiological/drug effects ; *Immunoglobulins/administration & dosage/pharmacology ; Biomarkers/blood ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.

METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.

RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.

CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.},
}

Humans
Pilot Projects
Male
Adult
Female
*Dietary Supplements
Double-Blind Method
*Exercise/physiology
*Respiratory Tract Infections/prevention & control/immunology/epidemiology
Gastrointestinal Microbiome/drug effects
*Stress, Physiological/drug effects
*Immunoglobulins/administration & dosage/pharmacology
Biomarkers/blood
Young Adult
Middle Aged

@article {pmid41683205,
year = {2026},
author = {Yu, W and Tang, K and An, R and Ma, S and Tan, H and Chen, M},
title = {Study on Association Between Gut Microbiota, Serum Metabolism and Gestational Diabetes Mellitus Based on Metagenomic and Metabolomics Analysis.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/nu18030381},
pmid = {41683205},
issn = {2072-6643},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/blood/metabolism ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; Adult ; *Metabolomics/methods ; *Metagenomics ; Feces/microbiology ; Pregnancy Trimester, First ; },
abstract = {Background/Objectives: This study aimed to explore the association between maternal gut microbiota and metabolic profiles in the first trimester and the subsequent risk of gestational diabetes mellitus (GDM), as well as to characterize association patterns linking gut microbiota, serum metabolites, and metabolic traits. Methods: A nested case-control study was conducted among women with GDM (n = 47) and those without GDM (n = 94). Metagenomic sequencing was applied to analyze fecal microbiota, and liquid chromatography-mass spectrometry (LC-MS) was used for non-targeted plasma metabolomics. Differential microbiota and metabolites between groups were identified, and correlation analyses were conducted to assess their associations with clinical indicators. Results: Women who later developed GDM showed lower alpha diversity and higher beta diversity. Eleven differential species were identified, with Collinsella aerofaciens and Clostridium bartlettii enriched in GDM, while nine species such as Alistipes putredinis and Bacteroidales bacterium ph8 were enriched in controls. Sixty-four plasma metabolites differed between groups, including increased glycerol-3-phosphate, aromatic amino acids, and glycerophosphocholine, and decreased cysteine, tryptophan, niacinamide, and stearic acid. Correlation analyses revealed significant relationships between Alistipes putredinis, Eubacterium eligens, and Bacteroidales bacterium ph8 with metabolic and clinical indicators (e.g., TG, TC, LDL). Conclusions: In this nested case-control study, women who later developed GDM exhibited reduced gut microbial diversity and altered metabolic profiles during the first trimester of pregnancy. Several microbial taxa and microbiota-metabolite associations were observed in relation to subsequent GDM status, highlighting early-pregnancy microbial and metabolic features that may be relevant to GDM-related metabolic changes.},
}

Humans
Female
*Diabetes, Gestational/microbiology/blood/metabolism
Pregnancy
*Gastrointestinal Microbiome/physiology
Case-Control Studies
Adult
*Metabolomics/methods
*Metagenomics
Feces/microbiology
Pregnancy Trimester, First

@article {pmid41680567,
year = {2026},
author = {Chen, L and Hong, C and Xie, Y},
title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {76},
pmid = {41680567},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; },
abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.},
}

Humans
*Sarcopenia/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use
Aged
Muscle Strength

@article {pmid41679837,
year = {2026},
author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y},
title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124919},
doi = {10.1016/j.carbpol.2026.124919},
pmid = {41679837},
issn = {1879-1344},
mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Amylose/chemistry/metabolism ; *Pyrobaculum/enzymology ; *Starch/chemistry ; Hot Temperature ; Hydrolysis ; Hydrogen-Ion Concentration ; },
abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.},
}

*Glycogen Debranching Enzyme System/metabolism/chemistry
*Amylose/chemistry/metabolism
*Pyrobaculum/enzymology
*Starch/chemistry
Hot Temperature
Hydrolysis
Hydrogen-Ion Concentration

@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}

*Gastrointestinal Microbiome/drug effects
*Galactans/chemistry/pharmacology/isolation & purification
Fermentation
*Agaricales/chemistry
Molecular Docking Simulation
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid41593440,
year = {2026},
author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F},
title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.},
journal = {The American journal of Chinese medicine},
volume = {54},
number = {1},
pages = {65-85},
doi = {10.1142/S0192415X26500023},
pmid = {41593440},
issn = {1793-6853},
mesh = {*Gastrointestinal Microbiome/immunology/physiology ; Humans ; *Myasthenia Gravis/immunology/therapy/microbiology ; *Neuroimmunomodulation ; Dysbiosis/immunology ; Probiotics ; *Brain/immunology ; Fecal Microbiota Transplantation ; Animals ; *Brain-Gut Axis/immunology ; },
abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.},
}

*Gastrointestinal Microbiome/immunology/physiology
Humans
*Myasthenia Gravis/immunology/therapy/microbiology
*Neuroimmunomodulation
Dysbiosis/immunology
Probiotics
*Brain/immunology
Fecal Microbiota Transplantation
Animals
*Brain-Gut Axis/immunology

@article {pmid41548304,
year = {2026},
author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T},
title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141134},
doi = {10.1016/j.jhazmat.2026.141134},
pmid = {41548304},
issn = {1873-3336},
mesh = {*Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Microbial Interactions ; Bacteria/genetics ; Genes, Bacterial ; Microbiota ; China ; Water Microbiology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.},
}

*Rivers/microbiology/chemistry
*Drug Resistance, Microbial/genetics
*Microbial Interactions
Bacteria/genetics
Genes, Bacterial
Microbiota
China
Water Microbiology
*Drug Resistance, Bacterial/genetics

@article {pmid41544592,
year = {2026},
author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J},
title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141133},
doi = {10.1016/j.jhazmat.2026.141133},
pmid = {41544592},
issn = {1873-3336},
mesh = {*Microplastics/metabolism/analysis/chemistry ; *Rivers/microbiology/chemistry ; Biofilms ; *Water Pollutants, Chemical/metabolism/analysis ; Bacteria/genetics/metabolism ; Polyvinyl Chloride/chemistry ; *Microbiota ; Polyesters/chemistry ; Biodegradation, Environmental ; Water Microbiology ; Cities ; },
abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.},
}

*Microplastics/metabolism/analysis/chemistry
*Rivers/microbiology/chemistry
Biofilms
*Water Pollutants, Chemical/metabolism/analysis
Bacteria/genetics/metabolism
Polyvinyl Chloride/chemistry
*Microbiota
Polyesters/chemistry
Biodegradation, Environmental
Water Microbiology
Cities

@article {pmid41537457,
year = {2026},
author = {Chari, NR and DeAngelis, KM and Aguilar, AA and Chan, ALH and Burgin, GA and Frey, SD and Taylor, BN},
title = {Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag002},
pmid = {41537457},
issn = {1751-7370},
support = {DEB-1456610//Long-Term Research in Environmental Biology/ ; DEB-1832110//U.S. National Science Foundation (NSF) Long-Term Ecological Research Program/ ; },
mesh = {*Plant Roots/metabolism/microbiology ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; *Biomass ; Soil/chemistry ; Carbon/metabolism ; *Bacteria/genetics/classification ; *Plant Exudates/metabolism ; Climate Change ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; Forests ; *Microbiota ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.},
}

*Plant Roots/metabolism/microbiology
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
*Biomass
Soil/chemistry
Carbon/metabolism
*Bacteria/genetics/classification
*Plant Exudates/metabolism
Climate Change
Metagenomics
DNA, Bacterial/genetics/chemistry
Forests
*Microbiota
DNA, Ribosomal/chemistry/genetics

@article {pmid41529631,
year = {2026},
author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H},
title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141112},
doi = {10.1016/j.jhazmat.2026.141112},
pmid = {41529631},
issn = {1873-3336},
mesh = {Seasons ; Animals ; *Lagomorpha/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Bacteria/genetics ; },
abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.},
}

Seasons
Animals
*Lagomorpha/microbiology/genetics
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
Bacteria/genetics

@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Nitrosamines/metabolism ; Bacteria/metabolism/genetics ; Multiomics ; Triazines ; },
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}

*Water Pollutants, Chemical/metabolism
*Microbiota
Biodegradation, Environmental
*Nitrosamines/metabolism
Bacteria/metabolism/genetics
Multiomics
Triazines

@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
mesh = {Animals ; *Aflatoxin B1/toxicity ; Bees/drug effects/microbiology/genetics ; Metagenomics ; Transcriptome/drug effects ; Gene Expression Profiling ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}

Animals
*Aflatoxin B1/toxicity
Bees/drug effects/microbiology/genetics
Metagenomics
Transcriptome/drug effects
Gene Expression Profiling
Gastrointestinal Microbiome/drug effects

@article {pmid41255157,
year = {2026},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {38},
number = {9},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Lipopolysaccharides/chemistry/metabolism ; *Hydrogels/chemistry/pharmacology ; Mice ; *Toll-Like Receptor 4/metabolism ; Polymyxin B/chemistry/pharmacology ; *Microbiota/drug effects ; Humans ; Mice, Inbred C57BL ; Wound Healing/drug effects ; Polyethyleneimine/chemistry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}

Animals
*Lipopolysaccharides/chemistry/metabolism
*Hydrogels/chemistry/pharmacology
Mice
*Toll-Like Receptor 4/metabolism
Polymyxin B/chemistry/pharmacology
*Microbiota/drug effects
Humans
Mice, Inbred C57BL
Wound Healing/drug effects
Polyethyleneimine/chemistry
RNA, Ribosomal, 16S/genetics

@article {pmid41678593,
year = {2026},
author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH},
title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.},
journal = {Circulation research},
volume = {138},
number = {4},
pages = {e326978},
doi = {10.1161/CIRCRESAHA.125.326978},
pmid = {41678593},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; },
abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Myocardium/metabolism/pathology
*Regeneration
*Heart/physiology

@article {pmid41677732,
year = {2026},
author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, ÉS},
title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/biology15030261},
pmid = {41677732},
issn = {2079-7737},
support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&I//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; },
abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.},
}

@article {pmid41674272,
year = {2026},
author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K},
title = {An ensemble binning approach to identify functional diversity in cleanroom environments.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {384},
number = {2314},
pages = {},
doi = {10.1098/rsta.2024.0438},
pmid = {41674272},
issn = {1471-2962},
support = {//UK Space Agency/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Metagenome ; *Environment, Controlled ; Spacecraft ; },
abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.},
}

*Microbiota/genetics
*Bacteria/genetics/classification/metabolism
Metagenomics/methods
Metagenome
*Environment, Controlled
Spacecraft

@article {pmid41674065,
year = {2026},
author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY},
title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510010},
doi = {10.4014/jmb.2510.10010},
pmid = {41674065},
issn = {1738-8872},
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Female ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Adult ; DNA, Bacterial/genetics ; Aged ; Biodiversity ; Case-Control Studies ; Sequence Analysis, DNA ; Skin Microbiome ; },
abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.},
}

Humans
*Sjogren's Syndrome/microbiology
*Skin/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Female
Middle Aged
Male
*Bacteria/classification/genetics/isolation & purification
Adult
DNA, Bacterial/genetics
Aged
Biodiversity
Case-Control Studies
Sequence Analysis, DNA
Skin Microbiome

@article {pmid41673713,
year = {2026},
author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ},
title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {65},
pmid = {41673713},
issn = {2049-2618},
support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Biofilms/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Droughts ; *Microbiota ; *Rivers/microbiology ; Metagenomics/methods ; Metagenome ; Switzerland ; Diatoms/genetics ; Viruses/classification/genetics/isolation & purification ; Cyanobacteria/genetics/classification ; },
abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.

RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.

CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.},
}

*Biofilms/growth & development
*Bacteria/classification/genetics/isolation & purification/metabolism
*Droughts
*Microbiota
*Rivers/microbiology
Metagenomics/methods
Metagenome
Switzerland
Diatoms/genetics
Viruses/classification/genetics/isolation & purification
Cyanobacteria/genetics/classification

@article {pmid41672513,
year = {2026},
author = {Nishijima, S and Hattori, M and Nagata, N},
title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {102},
number = {2},
pages = {82-103},
doi = {10.2183/pjab.102.006},
pmid = {41672513},
issn = {1349-2896},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Japan ; *Health ; *Disease ; East Asian People ; },
abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.},
}

Humans
*Gastrointestinal Microbiome/genetics
Japan
*Health
*Disease
East Asian People

@article {pmid41670415,
year = {2026},
author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A},
title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.},
journal = {Investigative ophthalmology & visual science},
volume = {67},
number = {2},
pages = {27},
doi = {10.1167/iovs.67.2.27},
pmid = {41670415},
issn = {1552-5783},
mesh = {*Gastrointestinal Microbiome/genetics/physiology ; Animals ; Humans ; *Retinitis Pigmentosa/microbiology/physiopathology ; Mice ; Female ; Male ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Disease Models, Animal ; Phenotype ; Adult ; Feces/microbiology ; Electroretinography ; Anti-Bacterial Agents/pharmacology ; Tomography, Optical Coherence ; Aged ; Mice, Inbred C57BL ; *Bacteria/genetics/isolation & purification ; },
abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.

METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The α and β diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.

RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1β, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.

CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.},
}

*Gastrointestinal Microbiome/genetics/physiology
Animals
Humans
*Retinitis Pigmentosa/microbiology/physiopathology
Mice
Female
Male
Disease Progression
RNA, Ribosomal, 16S/genetics
Middle Aged
Disease Models, Animal
Phenotype
Adult
Feces/microbiology
Electroretinography
Anti-Bacterial Agents/pharmacology
Tomography, Optical Coherence
Aged
Mice, Inbred C57BL
*Bacteria/genetics/isolation & purification

@article {pmid41669550,
year = {2026},
author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A},
title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20648},
pmid = {41669550},
issn = {2167-8359},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Nutrients ; *Stress, Physiological ; Phylogeny ; Biodegradation, Environmental ; },
abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Araceae/microbiology
*Bacteria/genetics/classification
*Nutrients
*Stress, Physiological
Phylogeny
Biodegradation, Environmental

@article {pmid41621514,
year = {2026},
author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G},
title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.},
journal = {International journal of biological macromolecules},
volume = {346},
number = {},
pages = {150646},
doi = {10.1016/j.ijbiomac.2026.150646},
pmid = {41621514},
issn = {1879-0003},
mesh = {*Probiotics/administration & dosage/pharmacology/chemistry ; *Chitosan/chemistry ; *Mannans/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/drug effects/metabolism ; Animals ; Microspheres ; *Cellulose/chemistry ; Intestinal Mucosa/metabolism ; *Drug Delivery Systems ; Oxidation-Reduction ; Humans ; Sulfhydryl Compounds/chemistry ; },
abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.},
}

*Probiotics/administration & dosage/pharmacology/chemistry
*Chitosan/chemistry
*Mannans/chemistry
*Gastrointestinal Microbiome/drug effects
*Colon/microbiology/drug effects/metabolism
Animals
Microspheres
*Cellulose/chemistry
Intestinal Mucosa/metabolism
*Drug Delivery Systems
Oxidation-Reduction
Humans
Sulfhydryl Compounds/chemistry

@article {pmid41621269,
year = {2026},
author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L},
title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.},
journal = {Water research},
volume = {293},
number = {},
pages = {125448},
doi = {10.1016/j.watres.2026.125448},
pmid = {41621269},
issn = {1879-2448},
mesh = {*Antimony/metabolism ; *Geologic Sediments/microbiology/chemistry ; Water Pollutants, Chemical ; *Amaranthaceae/growth & development/metabolism ; Microbiota ; Biodegradation, Environmental ; },
abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.},
}

*Antimony/metabolism
*Geologic Sediments/microbiology/chemistry
Water Pollutants, Chemical
*Amaranthaceae/growth & development/metabolism
Microbiota
Biodegradation, Environmental

@article {pmid41616776,
year = {2026},
author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W},
title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.},
journal = {Cell host & microbe},
volume = {34},
number = {2},
pages = {201-211.e6},
doi = {10.1016/j.chom.2026.01.006},
pmid = {41616776},
issn = {1934-6069},
mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Rhizosphere ; *Microbial Interactions ; *Soil/parasitology ; Microbiota ; *Eukaryota/physiology ; Metagenomics ; },
abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.},
}

*Soil Microbiology
*Bacteria/metabolism/genetics/classification
Rhizosphere
*Microbial Interactions
*Soil/parasitology
Microbiota
*Eukaryota/physiology
Metagenomics

@article {pmid41578124,
year = {2026},
author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M},
title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6070},
pmid = {41578124},
issn = {2045-2322},
support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics ; *Neoplasms/microbiology ; *Phosphorus-Oxygen Lyases/metabolism/genetics ; Female ; Male ; },
abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/enzymology/genetics
*Neoplasms/microbiology
*Phosphorus-Oxygen Lyases/metabolism/genetics
Female
Male

@article {pmid41570646,
year = {2026},
author = {Sidikjan, N and Li, Y and Chen, Y and Guo, XP and Liu, M and Huang, Y},
title = {Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways.},
journal = {Ecotoxicology and environmental safety},
volume = {310},
number = {},
pages = {119769},
doi = {10.1016/j.ecoenv.2026.119769},
pmid = {41570646},
issn = {1090-2414},
mesh = {*Biofilms/drug effects ; *Estuaries ; *Metals, Heavy/toxicity/analysis ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Genes, Bacterial ; Geologic Sediments/microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; },
abstract = {Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT, pbrA, cadD, and czcD. These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress.},
}

*Biofilms/drug effects
*Estuaries
*Metals, Heavy/toxicity/analysis
*Water Pollutants, Chemical/analysis/toxicity
China
Environmental Monitoring
Genes, Bacterial
Geologic Sediments/microbiology
Drug Resistance, Microbial/genetics
Microbiota

@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {33},
number = {4},
pages = {1447-1458},
pmid = {41569365},
issn = {1614-7499},
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Portugal ; *Soil Microbiology ; *Microplastics/analysis ; Soil/chemistry ; *Soil Pollutants/analysis ; Environmental Monitoring ; Microbiota ; Bacteria ; },
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}

*Polycyclic Aromatic Hydrocarbons/analysis
Portugal
*Soil Microbiology
*Microplastics/analysis
Soil/chemistry
*Soil Pollutants/analysis
Environmental Monitoring
Microbiota
Bacteria

@article {pmid41565669,
year = {2026},
author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J},
title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {45},
pmid = {41565669},
issn = {2055-5008},
support = {101019223/ERC_/European Research Council/International ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Trichuriasis/microbiology/parasitology/epidemiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Trichuris ; Tanzania/epidemiology ; Animals ; Laos/epidemiology ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; Female ; Feces/microbiology ; Male ; Adult ; Mucins/metabolism ; },
abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.},
}

Humans
*Gastrointestinal Microbiome
*Trichuriasis/microbiology/parasitology/epidemiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Trichuris
Tanzania/epidemiology
Animals
Laos/epidemiology
Metagenomics/methods
Fatty Acids, Volatile/metabolism
Female
Feces/microbiology
Male
Adult
Mucins/metabolism

@article {pmid41555453,
year = {2026},
author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M},
title = {Spatial and temporal patterns of public transit aerobiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {64},
pmid = {41555453},
issn = {2049-2618},
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Humans ; *Air Microbiology ; Metagenomics/methods ; *Microbiota/genetics ; Cities ; Seasons ; Biodiversity ; Spatio-Temporal Analysis ; },
abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.

RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.

CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.},
}

*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Humans
*Air Microbiology
Metagenomics/methods
*Microbiota/genetics
Cities
Seasons
Biodiversity
Spatio-Temporal Analysis

@article {pmid41554846,
year = {2026},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A},
title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5761},
pmid = {41554846},
issn = {2045-2322},
support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; },
mesh = {Animals ; Larva/microbiology/drug effects/growth & development ; *Disinfection/methods ; *Microbiota/drug effects ; *Ovum/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology/growth & development ; Disinfectants/pharmacology ; Bacteria/genetics/classification/drug effects ; },
abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.},
}

Animals
Larva/microbiology/drug effects/growth & development
*Disinfection/methods
*Microbiota/drug effects
*Ovum/microbiology/drug effects
RNA, Ribosomal, 16S/genetics
*Fishes/microbiology/growth & development
Disinfectants/pharmacology
Bacteria/genetics/classification/drug effects

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {31},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
mesh = {Animals ; *Prion Diseases/microbiology/prevention & control/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Catechin/analogs & derivatives/pharmacology ; Mice ; Mice, Inbred C57BL ; Biomarkers ; Male ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

Animals
*Prion Diseases/microbiology/prevention & control/drug therapy
*Gastrointestinal Microbiome/drug effects
*Catechin/analogs & derivatives/pharmacology
Mice
Mice, Inbred C57BL
Biomarkers
Male

@article {pmid41015591,
year = {2026},
author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A},
title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {399},
number = {2},
pages = {2081-2095},
pmid = {41015591},
issn = {1432-1912},
mesh = {Humans ; *One Health ; Animals ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.},
}

Humans
*One Health
Animals
*Drug Resistance, Bacterial/genetics
*Microbiota
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects

@article {pmid41668733,
year = {2025},
author = {Sui, Q and Yu, J and Cui, S},
title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1707599},
pmid = {41668733},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Male ; Female ; Aged ; Retrospective Studies ; *Atherosclerosis/microbiology/diagnosis ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Risk Factors ; Bacteria/classification/genetics/isolation & purification ; *Cardiovascular Diseases/microbiology/diagnosis ; Metagenomics ; },
abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.

METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).

RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.

CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.},
}

Humans
Middle Aged
Male
Female
Aged
Retrospective Studies
*Atherosclerosis/microbiology/diagnosis
*Microbiota
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
ROC Curve
Risk Factors
Bacteria/classification/genetics/isolation & purification
*Cardiovascular Diseases/microbiology/diagnosis
Metagenomics

@article {pmid41668731,
year = {2025},
author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C},
title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1745848},
pmid = {41668731},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; },
abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.

METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.

RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that the gut microbial richness of male individuals was significantly higher than that of females, and the β-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.

DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.},
}

Animals
*Gastrointestinal Microbiome/genetics
Female
Male
*Culex/microbiology/genetics/physiology
Metagenomics
*Smell/genetics
Gene Expression Profiling
Arthropod Antennae/metabolism
Transcriptome
Computational Biology
Multiomics

@article {pmid41667397,
year = {2026},
author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E},
title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2627692},
doi = {10.1080/19490976.2026.2627692},
pmid = {41667397},
issn = {1949-0984},
mesh = {Humans ; *Ceftriaxone/therapeutic use/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy ; Aged ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification ; Genetic Variation ; Adult ; Rectum/microbiology ; },
abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.},
}

Humans
*Ceftriaxone/therapeutic use/pharmacology
*beta-Lactamases/genetics/metabolism
*Anti-Bacterial Agents/therapeutic use/pharmacology
Male
Female
Middle Aged
Prospective Studies
*Gastrointestinal Microbiome/drug effects
*Enterobacteriaceae Infections/microbiology/drug therapy
Aged
*Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification
Genetic Variation
Adult
Rectum/microbiology

@article {pmid41665263,
year = {2026},
author = {Hutchinson, TF and Holland, SR and Clarke, DA and Ricci, F and Jirapanjawat, T and Leung, PM and Lappan, R and Liu, WPA and Bay, SK and Bliss, A and McGeoch, MA and Chown, SL and Greening, C},
title = {Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag020},
pmid = {41665263},
issn = {1751-7370},
abstract = {Polar desert soils host diverse microbial communities despite limited nutrients and frequent temperature and light fluctuations. Adapting to these extremes, most bacteria possess high-affinity hydrogenases and carbon monoxide dehydrogenases, enabling them to use atmospheric trace gases such as hydrogen (H2) and carbon monoxide (CO) to generate energy and fix carbon (aerotrophy). Despite the foundational importance of this process in polar desert ecosystems, little is known about the thermal sensitivity of trace gas oxidation or how this process will respond to climate warming. Here, we show through in situ and ex situ incubations that H2 consumption is an exceptionally thermally resilient process that can occur from -20 to +75°C, at rates comparable to temperate ecosystems (peaking at 8.56 nmol H2 h-1 g dry soil-1 at 25°C). Temperature ranges of CO (-20 to 42°C) and methane (CH4; -20 to 30°C) oxidation are also wider than expected, though thermal sensitivity patterns conform with general theory. Metagenomic analyses, including generation of 554 medium- to high-quality metagenome-assembled genomes, support these data, revealing that aerotrophs are widespread, diverse, and abundant, and suggesting most Antarctic bacteria function below their temperature optima for these processes. Modelling of seasonal temperatures across ice-free Antarctica under current and future emissions scenarios indicates that H2 and CO oxidation can occur year-round, increasing by up to 35% or 44%, respectively, by 2100. Our results indicate constitutive aerotrophic activity contributing to Antarctic ecosystem functioning and biodiversity across spatial and temporal scales, with further studies required to understand how it interacts with photosynthesis in a changing climate.},
}

@article {pmid41664936,
year = {2026},
author = {Shaikh-Ibrahim, A and De Lise, F and Curci, N and Gargano, M and Sacco, O and Di Fenza, M and Moracci, M and Cobucci-Ponzano, B},
title = {A Hyperthermostable Archaeal GH78 Rhamnosidase Efficiently Hydrolyzes Flavonoid Glycosides for Juice Debittering.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c16422},
pmid = {41664936},
issn = {1520-5118},
abstract = {α-L-Rhamnosidases are a class of glycosyl hydrolases (GHs) that catalyze the hydrolysis of terminal α-L-rhamnose residues from diverse glycoconjugates. While extensively characterized in bacterial and fungal sources, no archaeal α-L-rhamnosidases have been characterized to date. Herein, we report the identification and characterization of the first thermostable archaeal α-L-rhamnosidase (ArRha), derived from the metagenomic data set of Pisciarelli solfatara hot spring. ArRha, classified in glycoside hydrolase family GH78, efficiently hydrolyzes α-1,2 and α-1,6 rhamnosyl linkages in flavonoid glycosides with notable biological activities. The novel enzyme showed remarkable temperature stability, wide-range pH activity, organic solvent tolerance, and no metal dependence. Combined with a thermostable β-glucosidase, ArRha converts naringin to prunin and naringenin in sweet and blood orange juices, achieving >95% conversion within 2 h at 65 °C. This represents the first report of a hyperthermostable archaeal GH78 α-L-rhamnosidase with promising applications in industrial enzymatic juice debittering and sustainable flavonoid biotransformation.},
}

@article {pmid41619556,
year = {2026},
author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y},
title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157875},
doi = {10.1016/j.phymed.2026.157875},
pmid = {41619556},
issn = {1618-095X},
mesh = {Animals ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; *Diarrhea/drug therapy ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; *Sesquiterpenes/pharmacology ; Fatty Acids, Volatile/metabolism ; Disease Models, Animal ; Lactobacillus/drug effects ; Mice, Inbred C57BL ; *Lactones/pharmacology ; *Saponins/pharmacology ; Spleen/drug effects ; },
abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.

PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.

METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.

RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.

CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.},
}

Animals
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Signal Transduction/drug effects
NF-kappa B/metabolism
*Diarrhea/drug therapy
Mice
Receptors, G-Protein-Coupled/metabolism
Gastrointestinal Microbiome/drug effects
Male
*Sesquiterpenes/pharmacology
Fatty Acids, Volatile/metabolism
Disease Models, Animal
Lactobacillus/drug effects
Mice, Inbred C57BL
*Lactones/pharmacology
*Saponins/pharmacology
Spleen/drug effects

@article {pmid41619464,
year = {2026},
author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A},
title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181482},
doi = {10.1016/j.scitotenv.2026.181482},
pmid = {41619464},
issn = {1879-1026},
mesh = {*Palm Oil ; *Hydrogen/metabolism ; *Microbial Consortia ; *Petroleum/metabolism ; Biodegradation, Environmental ; Bioreactors ; Oil and Gas Fields ; Hydrocarbons/metabolism ; Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/metabolism ; },
abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.},
}

*Palm Oil
*Hydrogen/metabolism
*Microbial Consortia
*Petroleum/metabolism
Biodegradation, Environmental
Bioreactors
Oil and Gas Fields
Hydrocarbons/metabolism
Waste Disposal, Fluid/methods
*Water Pollutants, Chemical/metabolism

@article {pmid41576939,
year = {2026},
author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H},
title = {Microbiota from young mice restore the function of aged ISCs.},
journal = {Stem cell reports},
volume = {21},
number = {2},
pages = {102788},
doi = {10.1016/j.stemcr.2025.102788},
pmid = {41576939},
issn = {2213-6711},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Aging ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Mice, Inbred C57BL ; Basic Helix-Loop-Helix Proteins/metabolism/genetics ; Regeneration ; *Microbiota ; Akkermansia ; },
abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Aging
*Stem Cells/metabolism/cytology
Wnt Signaling Pathway
*Intestinal Mucosa/microbiology/metabolism/cytology
Mice, Inbred C57BL
Basic Helix-Loop-Helix Proteins/metabolism/genetics
Regeneration
*Microbiota
Akkermansia

@article {pmid41557465,
year = {2026},
author = {Ivanov, A and Popov, V and Morozov, M and Olekhnovich, E and Ulyantsev, V},
title = {MetaFX: feature extraction from whole-genome metagenomic sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {2},
pages = {},
doi = {10.1093/bioinformatics/btag018},
pmid = {41557465},
issn = {1367-4811},
support = {23-75-10125//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; *Whole Genome Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Metagenome ; Machine Learning ; Inflammatory Bowel Diseases/microbiology ; Databases, Genetic ; },
abstract = {MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers.

RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average.

MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.},
}

*Metagenomics/methods
Humans
*Software
*Whole Genome Sequencing/methods
Gastrointestinal Microbiome/genetics
*Metagenome
Machine Learning
Inflammatory Bowel Diseases/microbiology
Databases, Genetic

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {40},
pmid = {41526362},
issn = {2055-5008},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Virulence Factors/genetics ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation & purification ; Cohort Studies ; Metagenome ; },
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

*Colorectal Neoplasms/microbiology
Humans
*Gastrointestinal Microbiome
Metagenomics/methods
Virulence Factors/genetics
*Bacteria/genetics/drug effects/classification/pathogenicity/isolation & purification
Cohort Studies
Metagenome

@article {pmid41372407,
year = {2026},
author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N},
title = {Gut micro-organisms associated with health, nutrition and dietary interventions.},
journal = {Nature},
volume = {650},
number = {8101},
pages = {450-458},
pmid = {41372407},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Diet ; Male ; Female ; United Kingdom ; Body Mass Index ; Risk Factors ; United States ; *Health ; Middle Aged ; *Nutritional Status ; Adult ; Metagenomics ; },
abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
*Diet
Male
Female
United Kingdom
Body Mass Index
Risk Factors
United States
*Health
Middle Aged
*Nutritional Status
Adult
Metagenomics

@article {pmid41664657,
year = {2026},
author = {Chuckran, PF and Blazewicz, SJ and Ceja-Navarro, JA and Pett-Ridge, J and Schwartz, E and Dijkstra, P},
title = {The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20641},
pmid = {41664657},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Transcription, Genetic ; *Microbiota/genetics ; Glucose/metabolism ; Codon Usage ; Carbon/metabolism ; },
abstract = {Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.},
}

*Soil Microbiology
*Transcription, Genetic
*Microbiota/genetics
Glucose/metabolism
Codon Usage
Carbon/metabolism

@article {pmid41660616,
year = {2025},
author = {Liu, H and Liang, L and Wang, C and Luo, R and Luo, Q and Huang, C},
title = {Gut mycobiota dysbiosis and an emergent state of "co-dysbiosis" are associated with IgE sensitization in children with comorbid allergic rhinitis and constipation.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1745580},
pmid = {41660616},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; Child ; *Rhinitis, Allergic/immunology/microbiology/epidemiology ; *Immunoglobulin E/immunology/blood ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; Child, Preschool ; *Constipation/immunology/microbiology/epidemiology ; Case-Control Studies ; *Fungi/immunology ; Comorbidity ; Pilot Projects ; *Mycobiome/immunology ; Metagenomics ; },
abstract = {BACKGROUND: The comorbidity of allergic rhinitis (AR) and functional constipation (FC), termed ARFC, implies shared gut-immune pathways. Although bacterial dysbiosis has been implicated, the role of the gut mycobiota (fungal community) in this specific comorbidity remains unexplored.

METHODS: This pilot case-control study characterized the gut mycobiota in 19 ARFC and 17 healthy control (HC) children aged 3-6 years using metagenomic sequencing. Fungal community structure, taxonomic composition, and correlations with IgE levels were analyzed. Cross-kingdom bacterial-fungal interaction networks were constructed, and functional potential was predicted.

RESULTS: Alpha diversity was comparable, whereas beta diversity revealed significant structural shifts in the ARFC gut mycobiota. Key immunomodulatory fungi, including Cenococcum, Dentiscutata, Ambispora, and Saccharomyces, were markedly depleted in ARFC. These taxa served as top discriminators in random forest models and exhibited significant inverse correlations with total and allergen-specific IgE levels. Cross-kingdom network analysis identified dramatic ecological restructuring: the HC network was characterized by prevalent competitive interactions, whereas the ARFC network shifted exclusively to positive correlations, a state termed "co-dysbiosis." No significant differences were observed in predicted KEGG functional pathways.

CONCLUSION: This study provides the first evidence that gut mycobiota dysbiosis-marked by depletion of immunoregulatory fungi and an ecological shift toward cooperative interkingdom interactions ("co-dysbiosis")-is associated with IgE sensitization in ARFC children. These findings position the gut mycobiota as a novel element of the gut-nose axis in allergic disease, warranting further investigation.},
}

Humans
*Dysbiosis/immunology/microbiology
Child
*Rhinitis, Allergic/immunology/microbiology/epidemiology
*Immunoglobulin E/immunology/blood
*Gastrointestinal Microbiome/immunology
Female
Male
Child, Preschool
*Constipation/immunology/microbiology/epidemiology
Case-Control Studies
*Fungi/immunology
Comorbidity
Pilot Projects
*Mycobiome/immunology
Metagenomics

@article {pmid41660426,
year = {2026},
author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K},
title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1754671},
pmid = {41660426},
issn = {2235-2988},
mesh = {*Androgens/biosynthesis/metabolism ; *Databases, Genetic ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Transketolase/genetics/metabolism ; *Clostridium/genetics/enzymology/metabolism ; *Microbiota ; Prostatic Neoplasms ; },
abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.},
}

*Androgens/biosynthesis/metabolism
*Databases, Genetic
Humans
*Gastrointestinal Microbiome/genetics
Male
Transketolase/genetics/metabolism
*Clostridium/genetics/enzymology/metabolism
*Microbiota
Prostatic Neoplasms

@article {pmid41650276,
year = {2026},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb6265},
pmid = {41650276},
issn = {2375-2548},
mesh = {*Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology ; Animals ; Humans ; Metagenome ; Phylogeny ; Genome, Viral ; Bacteroides/virology ; },
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

*Gastrointestinal Microbiome
*Bacteriophages/genetics/physiology
Animals
Humans
Metagenome
Phylogeny
Genome, Viral
Bacteroides/virology

@article {pmid41628276,
year = {2026},
author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E},
title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013576},
pmid = {41628276},
issn = {1935-2735},
mesh = {Animals ; *Virome ; *Metagenome ; *Triatominae/virology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; Species Specificity ; Texas ; Female ; Arizona ; Insect Vectors/virology ; New Mexico ; },
abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.},
}

Animals
*Virome
*Metagenome
*Triatominae/virology
*Viruses/genetics/classification/isolation & purification
Phylogeny
Species Specificity
Texas
Female
Arizona
Insect Vectors/virology
New Mexico

@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Fuentes Artiles, R and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {17},
number = {1},
pages = {24},
pmid = {41618437},
issn = {2042-6410},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Coronary Artery Disease/microbiology/metabolism ; *Sex Characteristics ; Female ; Male ; },
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Coronary Artery Disease/microbiology/metabolism
*Sex Characteristics
Female
Male

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1533},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Food Chain ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/metabolism/genetics/classification ; Microbiota ; Animals ; Phylogeny ; Metagenomics ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

*Food Chain
*Soil Microbiology
*Soil/chemistry
*Bacteria/metabolism/genetics/classification
Microbiota
Animals
Phylogeny
Metagenomics

@article {pmid41432253,
year = {2026},
author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C},
title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf286},
pmid = {41432253},
issn = {1751-7370},
support = {ECPF24-4273843556//Early Career Postdoctoral Fellowship/ ; //Faculty of Medicine, Nursing and Health Science at Monash University/ ; DE250101210//ARC DECRA Fellowships/ ; FT240100502//ARC Future Fellowship/ ; SR200100005//ARC SRIEAS/ ; //Securing Antarctica's Environmental Future/ ; },
mesh = {*Caves/microbiology ; *Bacteria/metabolism/genetics/classification ; *Geologic Sediments/microbiology ; *Archaea/metabolism/genetics/classification ; *Ecosystem ; Metagenome ; *Microbiota ; Photosynthesis ; Eukaryota/genetics/metabolism/classification ; Seawater/microbiology ; },
abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.},
}

*Caves/microbiology
*Bacteria/metabolism/genetics/classification
*Geologic Sediments/microbiology
*Archaea/metabolism/genetics/classification
*Ecosystem
Metagenome
*Microbiota
Photosynthesis
Eukaryota/genetics/metabolism/classification
Seawater/microbiology

@article {pmid41395693,
year = {2026},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity & metabolism},
volume = {28},
number = {3},
pages = {1826-1835},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestlé Health Science/ ; //Pierre Mercier Foundation/ ; },
mesh = {Humans ; *Diet, Ketogenic ; *Gastrointestinal Microbiome/physiology ; *Prediabetic State/microbiology/diet therapy/complications ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/diet therapy ; *Obesity, Morbid/microbiology/diet therapy/complications ; *Obesity/microbiology/diet therapy ; Caloric Restriction ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).

METHODS: In a randomised trial, patients with BMI >35 kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.

RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.

CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}

Humans
*Diet, Ketogenic
*Gastrointestinal Microbiome/physiology
*Prediabetic State/microbiology/diet therapy/complications
Male
Female
Middle Aged
Adult
Feces/microbiology
Diabetes Mellitus, Type 2/microbiology/diet therapy
*Obesity, Morbid/microbiology/diet therapy/complications
*Obesity/microbiology/diet therapy
Caloric Restriction

@article {pmid41649278,
year = {2026},
author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA},
title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117325},
doi = {10.1128/msystems.01173-25},
pmid = {41649278},
issn = {2379-5077},
abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.

IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.},
}

@article {pmid41616716,
year = {2026},
author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM},
title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.},
journal = {Journal of environmental management},
volume = {400},
number = {},
pages = {128747},
doi = {10.1016/j.jenvman.2026.128747},
pmid = {41616716},
issn = {1095-8630},
mesh = {*Manure/microbiology ; Animals ; Swine ; *Microbiota ; *Soil Microbiology ; Farms ; Soil ; Fertilizers ; Bacteria ; },
abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.},
}

*Manure/microbiology
Animals
Swine
*Microbiota
*Soil Microbiology
Farms
Soil
Fertilizers
Bacteria

@article {pmid41570486,
year = {2026},
author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K},
title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.},
journal = {Journal of neuroimmunology},
volume = {413},
number = {},
pages = {578870},
doi = {10.1016/j.jneuroim.2026.578870},
pmid = {41570486},
issn = {1872-8421},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; Animals ; *Neuroinflammatory Diseases/metabolism ; *Probiotics/administration & dosage ; *Cognitive Aging/physiology ; *Brain-Gut Axis/physiology/drug effects ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; },
abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.},
}

Humans
*Gastrointestinal Microbiome/physiology/drug effects
Animals
*Neuroinflammatory Diseases/metabolism
*Probiotics/administration & dosage
*Cognitive Aging/physiology
*Brain-Gut Axis/physiology/drug effects
*Brain/metabolism
*Dysbiosis/metabolism
*Aging

@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food & function},
volume = {17},
number = {3},
pages = {1451-1464},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Rutin/pharmacology/administration & dosage ; Male ; *Insulin Resistance ; *Glycation End Products, Advanced/adverse effects/metabolism ; Mice ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dietary Advanced Glycation End Products ; },
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Rutin/pharmacology/administration & dosage
Male
*Insulin Resistance
*Glycation End Products, Advanced/adverse effects/metabolism
Mice
Mice, Inbred C57BL
Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Fatty Acids, Volatile/metabolism
Dietary Advanced Glycation End Products

@article {pmid41545429,
year = {2026},
author = {Maharaj, SD and Nkuna, R and Matambo, TS},
title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5486},
pmid = {41545429},
issn = {2045-2322},
mesh = {*Sewage/microbiology/chemistry ; *Wastewater/microbiology/chemistry ; *Metagenomics/methods ; Bacteria/genetics/classification ; *Metagenome ; South Africa ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; High-Throughput Nucleotide Sequencing ; Biological Oxygen Demand Analysis ; Filtration ; Microbiota ; },
abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.},
}

*Sewage/microbiology/chemistry
*Wastewater/microbiology/chemistry
*Metagenomics/methods
Bacteria/genetics/classification
*Metagenome
South Africa
*Water Purification/methods
*Waste Disposal, Fluid/methods
High-Throughput Nucleotide Sequencing
Biological Oxygen Demand Analysis
Filtration
Microbiota

@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial taxonomic and functional responses to heavy metal gradients in mining-impacted stream sediments.},
journal = {Environmental research},
volume = {293},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Metals, Heavy/analysis/toxicity ; *Mining ; Archaea/drug effects/classification ; *Water Pollutants, Chemical/analysis/toxicity ; Bacteria/drug effects/classification ; *Rivers/microbiology/chemistry ; China ; Fungi/drug effects/classification ; *Microbiota/drug effects ; Environmental Monitoring ; },
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1 %, 12.4 %, and 12.9 % of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4 %) and Acidithiobacillus (5.0 %), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8 %) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}

*Geologic Sediments/microbiology/chemistry
*Metals, Heavy/analysis/toxicity
*Mining
Archaea/drug effects/classification
*Water Pollutants, Chemical/analysis/toxicity
Bacteria/drug effects/classification
*Rivers/microbiology/chemistry
China
Fungi/drug effects/classification
*Microbiota/drug effects
Environmental Monitoring

@article {pmid41499829,
year = {2026},
author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125312},
doi = {10.1016/j.watres.2025.125312},
pmid = {41499829},
issn = {1879-2448},
mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Carbon Cycle ; Eutrophication ; Carbon ; Microbial Interactions ; Microbiota ; },
abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.},
}

*Lakes/chemistry/microbiology
Seasons
*Carbon Cycle
Eutrophication
Carbon
Microbial Interactions
Microbiota

@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {60},
number = {12},
pages = {1237-1253},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Saliva/microbiology ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Feces/microbiology ; Female ; Metabolomics ; Adult ; Middle Aged ; *Mouth/microbiology ; Multiomics ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.

METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3 months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.

RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.

CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

Humans
*Gastrointestinal Microbiome
Saliva/microbiology
*Periodontitis/microbiology/therapy/metabolism
Male
Feces/microbiology
Female
Metabolomics
Adult
Middle Aged
*Mouth/microbiology
Multiomics

@article {pmid41645099,
year = {2026},
author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z},
title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04800-7},
pmid = {41645099},
issn = {1471-2180},
support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.},
}

@article {pmid41644290,
year = {2026},
author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y},
title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {2},
pages = {e70714},
doi = {10.1111/jocd.70714},
pmid = {41644290},
issn = {1473-2165},
support = {//Proya Cosmetics Co. Ltd/ ; },
mesh = {Humans ; Female ; *Sebum/metabolism ; *Lipidomics/methods ; *Scalp/microbiology/metabolism ; Young Adult ; Adult ; *Dermatitis, Seborrheic/microbiology ; Metagenomics ; Microbiota ; *Scalp Dermatoses/microbiology ; China ; Dandruff/microbiology ; Lipids/analysis ; Paper ; East Asian People ; },
abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.

AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.

METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.

RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).

CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.},
}

Humans
Female
*Sebum/metabolism
*Lipidomics/methods
*Scalp/microbiology/metabolism
Young Adult
Adult
*Dermatitis, Seborrheic/microbiology
Metagenomics
Microbiota
*Scalp Dermatoses/microbiology
China
Dandruff/microbiology
Lipids/analysis
Paper
East Asian People

@article {pmid41592403,
year = {2026},
author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C},
title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111660},
doi = {10.1016/j.ijfoodmicro.2026.111660},
pmid = {41592403},
issn = {1879-3460},
mesh = {Fermentation ; Metagenomics ; Metabolomics ; *Pichia/metabolism/genetics/classification ; China ; *Microbiota ; *Wine/microbiology/analysis ; Species Specificity ; },
abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.},
}

Fermentation
Metagenomics
Metabolomics
*Pichia/metabolism/genetics/classification
China
*Microbiota
*Wine/microbiology/analysis
Species Specificity

@article {pmid41592401,
year = {2026},
author = {Sandes, S and Figueiredo, N and Pires, S and Assis, D and Pedroso, S and Paiva, MJ and Neumann, E and Alvarenga, VO and Contreras-Castillo, CJ and Sant'Ana, AS},
title = {Lactic acid spraying on split carcasses reshapes microbial succession and reduces the occurrence of blown pack spoilage in vacuum-packaged beef stored at different temperatures over extended shelf life.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111659},
doi = {10.1016/j.ijfoodmicro.2026.111659},
pmid = {41592401},
issn = {1879-3460},
mesh = {Animals ; Food Packaging/methods ; Cattle ; Vacuum ; *Bacteria/drug effects/genetics/isolation & purification/classification/growth & development ; *Lactic Acid/pharmacology ; Temperature ; Food Storage ; Food Microbiology ; *Food Preservation/methods ; *Red Meat/microbiology ; Hydrogen-Ion Concentration ; Volatile Organic Compounds/analysis ; Microbiota/drug effects ; },
abstract = {Beef is a highly perishable product due to its high moisture content, neutral pH, and rich nutrient profile, which favor microbial growth and spoilage. While vacuum packaging extends shelf life by limiting aerobic bacteria, it may promote the proliferation of anaerobic and facultative anaerobic spoilage organisms, leading to blown pack spoilage. This study investigated the effects of lactic acid spraying on split carcasses categorized by two pH levels (high or ideal) on microbial succession and volatile organic compound (VOC) production in vacuum-packaged sirloins, stored at 0 °C, 4 °C, and 7 °C for up to 120 days. Using culture-based methods, 16S rRNA gene sequencing, and VOC profiling, it has been found that lactic acid treatment significantly reduced initial bacterial loads, especially in high-pH split carcasses (P < 0,05), and modulated microbial communities over time. Treated samples exhibited a lower incidence of blown pack spoilage (BPS) under specific storage time-temperature conditions. Nevertheless, bacterial changes under specific time-temperature storage conditions were characterized by a microbiota dominated by Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Carnobacterium, Hafnia-Obesumbacterium, and Serratia, regardless type of treatment. Overall microbial diversity was not significantly affected; however, the composition of dominant bacterial genera and VOC profiles differed between treated and non-treated groups, suggesting that specific bacterial taxa and compounds may serve as indicators of spoilage progression in vacuum-packed meat under defined storage conditions.},
}

Animals
Food Packaging/methods
Cattle
Vacuum
*Bacteria/drug effects/genetics/isolation & purification/classification/growth & development
*Lactic Acid/pharmacology
Temperature
Food Storage
Food Microbiology
*Food Preservation/methods
*Red Meat/microbiology
Hydrogen-Ion Concentration
Volatile Organic Compounds/analysis
Microbiota/drug effects

@article {pmid41582242,
year = {2026},
author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM},
title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5348},
pmid = {41582242},
issn = {2045-2322},
mesh = {*Solanum lycopersicum/virology/genetics/microbiology/growth & development ; *Endophytes/genetics/isolation & purification/classification ; *Begomovirus/pathogenicity ; *Plant Diseases/virology/genetics/microbiology ; *Disease Resistance/genetics ; Genotype ; Biodiversity ; Bacteria/isolation & purification/genetics/classification ; },
abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.},
}

*Solanum lycopersicum/virology/genetics/microbiology/growth & development
*Endophytes/genetics/isolation & purification/classification
*Begomovirus/pathogenicity
*Plant Diseases/virology/genetics/microbiology
*Disease Resistance/genetics
Genotype
Biodiversity
Bacteria/isolation & purification/genetics/classification

@article {pmid41547150,
year = {2026},
author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W},
title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111622},
doi = {10.1016/j.ijfoodmicro.2026.111622},
pmid = {41547150},
issn = {1879-3460},
mesh = {Animals ; Horses ; *Milk/microbiology ; Metagenomics ; *Lactobacillales/genetics/physiology ; Fermentation ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/classification/isolation & purification/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Female ; Food Microbiology ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.},
}

Animals
Horses
*Milk/microbiology
Metagenomics
*Lactobacillales/genetics/physiology
Fermentation
*Microbiota
*Drug Resistance, Microbial/genetics
Bacteria/genetics/classification/isolation & purification/drug effects
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Female
Food Microbiology

@article {pmid41535300,
year = {2026},
author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC},
title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {36},
pmid = {41535300},
issn = {2055-5008},
support = {NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; Pilot Projects ; Male ; *Autism Spectrum Disorder/microbiology/therapy/complications ; Female ; Child ; *Synbiotics/administration & dosage ; *Anxiety/therapy/microbiology ; Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics ; Treatment Outcome ; Bacteria/classification/genetics/isolation & purification ; Metabolomics ; },
abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.},
}

Humans
Pilot Projects
Male
*Autism Spectrum Disorder/microbiology/therapy/complications
Female
Child
*Synbiotics/administration & dosage
*Anxiety/therapy/microbiology
Gastrointestinal Microbiome
Feces/microbiology
Metagenomics
Treatment Outcome
Bacteria/classification/genetics/isolation & purification
Metabolomics

@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {61},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; Female ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Stress, Physiological ; Milk/metabolism ; Oxidative Stress ; Metabolomics ; Archaea/classification/genetics/isolation & purification ; Methane/metabolism ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Lactation/physiology
Female
*Gastrointestinal Microbiome
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification/metabolism
*Stress, Physiological
Milk/metabolism
Oxidative Stress
Metabolomics
Archaea/classification/genetics/isolation & purification
Methane/metabolism

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {60},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Gastrointestinal Microbiome ; Female ; Milk/chemistry/metabolism ; *Rectum/microbiology ; Metagenomics ; Lactation ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Dairying ; Longevity ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

Animals
Cattle
*Rumen/microbiology
*Gastrointestinal Microbiome
Female
Milk/chemistry/metabolism
*Rectum/microbiology
Metagenomics
Lactation
Metabolomics
Bacteria/classification/genetics/isolation & purification
Dairying
Longevity

@article {pmid41027803,
year = {2026},
author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU},
title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.},
journal = {Annals of the rheumatic diseases},
volume = {85},
number = {2},
pages = {254-264},
doi = {10.1016/j.ard.2025.08.029},
pmid = {41027803},
issn = {1468-2060},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/genetics/metabolism/diagnosis ; *Twins, Monozygotic ; *Fatty Acids, Volatile/metabolism/blood ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; Biomarkers/metabolism ; Feces/chemistry/microbiology ; Adult ; Aged ; },
abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.

METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.

RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.

CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.},
}

Humans
*Arthritis, Rheumatoid/microbiology/genetics/metabolism/diagnosis
*Twins, Monozygotic
*Fatty Acids, Volatile/metabolism/blood
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
Biomarkers/metabolism
Feces/chemistry/microbiology
Adult
Aged

@article {pmid41644119,
year = {2026},
author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG},
title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.},
journal = {Environmental microbiology},
volume = {28},
number = {2},
pages = {e70219},
doi = {10.1111/1462-2920.70219},
pmid = {41644119},
issn = {1462-2920},
support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/metabolism/genetics ; Photosynthesis ; Metagenome ; Microbiota ; Light ; },
abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.},
}

*Anthozoa/microbiology
Animals
Virulence
*Bacteria/metabolism/genetics/pathogenicity
*Cyanobacteria/metabolism/genetics
Photosynthesis
Metagenome
Microbiota
Light

@article {pmid41640872,
year = {2026},
author = {Chen, YX and Sun, NQ and Mo, SJ},
title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.},
journal = {World journal of gastroenterology},
volume = {32},
number = {4},
pages = {114468},
pmid = {41640872},
issn = {2219-2840},
mesh = {*NF-E2-Related Factor 2/metabolism ; Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Parkinson Disease/complications ; *Gastrointestinal Diseases/etiology/therapy/microbiology ; Mice ; Disease Models, Animal ; Kelch-Like ECH-Associated Protein 1/metabolism ; Signal Transduction/drug effects ; Fecal Microbiota Transplantation ; Brain-Gut Axis/drug effects ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; },
abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.},
}

*NF-E2-Related Factor 2/metabolism
Gastrointestinal Microbiome/drug effects
Animals
Humans
*Parkinson Disease/complications
*Gastrointestinal Diseases/etiology/therapy/microbiology
Mice
Disease Models, Animal
Kelch-Like ECH-Associated Protein 1/metabolism
Signal Transduction/drug effects
Fecal Microbiota Transplantation
Brain-Gut Axis/drug effects
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine

@article {pmid41640388,
year = {2026},
author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J},
title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72952},
pmid = {41640388},
issn = {2045-7758},
abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.},
}

@article {pmid41635749,
year = {2025},
author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É},
title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100333},
pmid = {41635749},
issn = {2667-114X},
abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.},
}

@article {pmid41632094,
year = {2026},
author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N},
title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag007},
pmid = {41632094},
issn = {1574-6941},
abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.},
}

@article {pmid41593363,
year = {2026},
author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL},
title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {359-374},
pmid = {41593363},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; },
mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; },
abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.},
}

*Bacteria/metabolism
Biomass
Bradyrhizobium/metabolism
Climate Change
Metagenome
Microbiota
Nitrogen/metabolism
*Nitrogen Compounds/metabolism
*Nitrogen Cycle
*Seasons
*Snow
*Soil Microbiology
Ecosystem
Multiomics

@article {pmid41581292,
year = {2026},
author = {Diehl, C and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Pastore, J and da Silveira Nicoloso, R and Dorn, M and Kich, JD and Siqueira, FM},
title = {Shaping soil fungal communities: How swine waste treatment systems and geography drive fungal community shifts.},
journal = {The Science of the total environment},
volume = {1015},
number = {},
pages = {181376},
doi = {10.1016/j.scitotenv.2026.181376},
pmid = {41581292},
issn = {1879-1026},
mesh = {Animals ; *Soil Microbiology ; Swine ; *Fungi/classification ; Brazil ; Fertilizers ; *Mycobiome ; Soil/chemistry ; Manure ; },
abstract = {The use of swine waste as an organic fertilizer is an important practice in sustainable agriculture. This study aims to evaluate the effects of two common swine waste treatment systems, Covered Lagoon Biodigesters (CLB) and Waste Stabilization Ponds (WSP), on fungal community structure in soil. Soil and waste samples were collected from swine farms across five Brazilian states, representing different geographical regions with distinct climate, soil types, and vegetation. A metagenomic approach was employed to analyze the fungal communities present in the samples. Our results revealed that fertilization with swine waste did not significantly affect the overall diversity of fungal communities, although distinct shifts in community composition were observed between fertilized and non-fertilized soils. Notably, reads assigned to Sugiyamaella lignohabitans were detected only in samples from waste stabilization ponds, suggesting that this environment may favor fungal taxa associated with lignocellulose degradation. Furthermore, the fungal genera Fusarium and Rhizophagus exhibited contrasting responses to fertilization, with Fusarium being more abundant in fertilized soils and Rhizophagus decreasing in abundance. Geographic variation in fungal community composition was also observed, correlating with the physicochemical properties of the soil. These findings indicate that, in our dataset, the waste treatment systems had little influence on the fungal diversity of waste samples, whereas soil fertilization with swine waste was associated with marked shifts in fungal community composition, particularly in terms of taxonomic structure.},
}

Animals
*Soil Microbiology
Swine
*Fungi/classification
Brazil
Fertilizers
*Mycobiome
Soil/chemistry
Manure

@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; *Microbial Consortia/physiology ; *Microbiota ; Bioreactors/microbiology ; Bacteria/metabolism ; },
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}

*Sewage/microbiology
*Fatty Acids/biosynthesis
*Microbial Consortia/physiology
*Microbiota
Bioreactors/microbiology
Bacteria/metabolism

@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {56},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
mesh = {Animals ; *Heteroptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Predatory Behavior ; Biological Evolution ; Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Symbiosis ; Adaptation, Physiological ; Feeding Behavior ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

Animals
*Heteroptera/microbiology/physiology
*Gastrointestinal Microbiome
*Predatory Behavior
Biological Evolution
Bacteria/classification/genetics/isolation & purification
Phylogeny
Symbiosis
Adaptation, Physiological
Feeding Behavior
RNA, Ribosomal, 16S/genetics

@article {pmid41490675,
year = {2026},
author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C},
title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133923},
doi = {10.1016/j.biortech.2026.133923},
pmid = {41490675},
issn = {1873-2976},
mesh = {*Odorants/prevention & control/analysis ; *Composting/methods ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Microbial Consortia ; *Bacteria/metabolism ; Hydrogen Sulfide ; Ammonia ; },
abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.},
}

*Odorants/prevention & control/analysis
*Composting/methods
*Nitrogen/metabolism
*Sulfur/metabolism
*Microbial Consortia
*Bacteria/metabolism
Hydrogen Sulfide
Ammonia

@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}

*Chagas Disease/microbiology/parasitology
Animals
Mice
Trypanosoma cruzi
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid41588163,
year = {2026},
author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P},
title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {442-460},
pmid = {41588163},
issn = {2058-5276},
support = {01EA1803//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Type III Secretion Systems/genetics/metabolism/immunology ; Bacterial Proteins/metabolism/genetics ; NF-kappa B/metabolism ; *Host-Pathogen Interactions/immunology ; Metagenomics ; *Host Microbial Interactions/immunology ; Cytokines/metabolism ; Protein Interaction Maps ; },
abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Type III Secretion Systems/genetics/metabolism/immunology
Bacterial Proteins/metabolism/genetics
NF-kappa B/metabolism
*Host-Pathogen Interactions/immunology
Metagenomics
*Host Microbial Interactions/immunology
Cytokines/metabolism
Protein Interaction Maps

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {415-428},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Feces/microbiology/chemistry ; *Ethanol/metabolism ; Male ; Female ; Middle Aged ; Adult ; Cohort Studies ; Metagenomics ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics ; Fermentation ; Bacteria/metabolism/genetics/classification/isolation & purification ; Proteobacteria/metabolism/genetics/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Alcoholic Intoxication/microbiology ; Klebsiella pneumoniae/metabolism/genetics ; Metabolomics ; Metabolic Networks and Pathways/genetics ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Feces/microbiology/chemistry
*Ethanol/metabolism
Male
Female
Middle Aged
Adult
Cohort Studies
Metagenomics
Fecal Microbiota Transplantation
Escherichia coli/metabolism/genetics
Fermentation
Bacteria/metabolism/genetics/classification/isolation & purification
Proteobacteria/metabolism/genetics/isolation & purification
Anti-Bacterial Agents/therapeutic use
*Alcoholic Intoxication/microbiology
Klebsiella pneumoniae/metabolism/genetics
Metabolomics
Metabolic Networks and Pathways/genetics

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology ; *Animal Feed/analysis ; *Poaceae/metabolism ; Fermentation ; Metagenomics ; *Dietary Fiber/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome ; Female ; Metabolomics ; Mongolia ; Digestion ; Fungi/classification/genetics/metabolism/isolation & purification ; Metagenome ; },
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

Animals
*Rumen/microbiology/metabolism
Cattle/microbiology
*Animal Feed/analysis
*Poaceae/metabolism
Fermentation
Metagenomics
*Dietary Fiber/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome
Female
Metabolomics
Mongolia
Digestion
Fungi/classification/genetics/metabolism/isolation & purification
Metagenome

@article {pmid41499920,
year = {2026},
author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S},
title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106558},
doi = {10.1016/j.clnu.2025.106558},
pmid = {41499920},
issn = {1532-1983},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Child ; Child, Preschool ; Female ; Male ; *Pediatric Obesity/microbiology ; Longitudinal Studies ; Cross-Sectional Studies ; Feces/microbiology ; Body Mass Index ; Risk Assessment ; *Thinness/microbiology ; Overweight/microbiology ; Cohort Studies ; Bacteria/classification ; },
abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.

METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.

RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.

CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.

CLINICALTRIALS: gov ID NCT06317883.},
}

Humans
*Gastrointestinal Microbiome/physiology
Child
Child, Preschool
Female
Male
*Pediatric Obesity/microbiology
Longitudinal Studies
Cross-Sectional Studies
Feces/microbiology
Body Mass Index
Risk Assessment
*Thinness/microbiology
Overweight/microbiology
Cohort Studies
Bacteria/classification

@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {54},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Propionates/metabolism ; Weaning ; Fermentation ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Stress, Physiological ; Animal Feed ; Liver/metabolism ; Metagenomics ; Gluconeogenesis ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.

RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n = 24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.

CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}

Animals
*Rumen/microbiology/metabolism
*Propionates/metabolism
Weaning
Fermentation
Sheep/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/metabolism/genetics/isolation & purification
*Stress, Physiological
Animal Feed
Liver/metabolism
Metagenomics
Gluconeogenesis

@article {pmid41467811,
year = {2026},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0303325},
doi = {10.1128/spectrum.03033-25},
pmid = {41467811},
issn = {2165-0497},
support = {NRFI09-0015//National Research Foundation Singapore/ ; CIRG22jul-0023//National Medical Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bifidobacterium/isolation & purification/genetics/classification ; Feces/microbiology ; *Single-Cell Analysis/methods ; Whole Genome Sequencing ; Genome, Bacterial ; Phylogeny ; },
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.

IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}

Humans
*Gastrointestinal Microbiome
*Bifidobacterium/isolation & purification/genetics/classification
Feces/microbiology
*Single-Cell Analysis/methods
Whole Genome Sequencing
Genome, Bacterial
Phylogeny

@article {pmid41451983,
year = {2026},
author = {Fan, Y and Ju, T and Bhardwaj, T and Korver, DR and Willing, BP},
title = {Chicken cecal microbial functional gene content and resistome differ by age and barn disinfection practice.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0373725},
doi = {10.1128/spectrum.03737-25},
pmid = {41451983},
issn = {2165-0497},
support = {RGPIN-2019-06336//Natural Sciences and Engineering Research Council of Canada/ ; //Agriculture Funding Consortium/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Disinfection/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; Disinfectants/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Age Factors ; Housing, Animal ; Metagenomics ; },
abstract = {Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Studies showed that disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functional gene content. The current study compared the effects of disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after two production cycles at seven barns. Shotgun metagenomic sequencing performed on cecal contents collected at days 7 and 30 also allowed the evaluation of age-associated characteristics of the microbiome. The age of the chickens had the largest effects on the resistome, with younger birds having higher relative abundance of total ARGs (P < 0.05) and differences in resistance mechanism; however, functional gene content and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically disinfected barns had decreased gene content related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically disinfected conditions (FDR-P < 0.05), suggesting the selection for stress resistance. Lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecal Helicobacter pullorum was observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P < 0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial gene function and resistome.IMPORTANCEThis is the first study to evaluate the effect of sanitation practices on microbial functional gene content and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology
*Disinfection/methods
*Gastrointestinal Microbiome/genetics/drug effects
Disinfectants/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Age Factors
Housing, Animal
Metagenomics