@article {pmid42351291,
year = {2026},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42351291},
issn = {2049-2618},
mesh = {Humans ; *Metagenome ; Shotgun Sequencing ; *Microbiota/genetics ; Child ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation ; Female ; },
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.},
}

Humans
*Metagenome
Shotgun Sequencing
*Microbiota/genetics
Child
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Molecular Sequence Annotation
Female

@article {pmid42576026,
year = {2026},
author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T},
title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.},
journal = {Nature genetics},
volume = {58},
number = {9},
pages = {2211-2225},
pmid = {42576026},
issn = {1546-1718},
support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology/epidemiology ; Japan/epidemiology ; *Mutation ; *Polyketides/adverse effects ; *Peptides ; Whole Genome Sequencing ; Prevalence ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; Feces/microbiology ; Gene Expression Profiling ; Risk Factors ; East Asian People ; },
abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.},
}

Humans
*Colorectal Neoplasms/genetics/microbiology/epidemiology
Japan/epidemiology
*Mutation
*Polyketides/adverse effects
*Peptides
Whole Genome Sequencing
Prevalence
Female
*Gastrointestinal Microbiome/genetics
Male
Middle Aged
Aged
Feces/microbiology
Gene Expression Profiling
Risk Factors
East Asian People

@article {pmid42580037,
year = {2026},
author = {Kearney, A and Chau, K and Kotay, S and Martin, J and Kirby, A and Mathers, AJ and Stoesser, N},
title = {Hospital sinks and healthcare-associated infection: ecology, transmission, surveillance and mitigation.},
journal = {EBioMedicine},
volume = {131},
number = {},
pages = {106415},
pmid = {42580037},
issn = {2352-3964},
mesh = {Humans ; *Cross Infection/transmission/epidemiology/prevention & control/microbiology ; *Infection Control/methods ; Hospitals ; Microbiota ; },
abstract = {Hospital sinks are recognised polymicrobial reservoirs for multi-drug resistant organisms and have been implicated in patient transmission and outbreaks. Earlier studies on sink-associated microbes predominantly focused on specific species or resistance mechanisms (e.g. carbapenemases) using targeted microbiological methods. More recently, less selective approaches (e.g. metagenomic sequencing) have enabled broader characterisation of these microbial communities. This review summarises current evidence describing hospital sink-trap microbiomes, examining ecological determinants, surveillance strategies and interventions aiming to mitigate transmission from these reservoirs. We discuss biotic and abiotic factors that shape microbial selection/persistence, assess approaches to managing these reservoirs to reduce patient risk, and highlight priorities for future research to inform evidence-based practice in healthcare settings.},
}

Humans
*Cross Infection/transmission/epidemiology/prevention & control/microbiology
*Infection Control/methods
Hospitals
Microbiota

@article {pmid42603474,
year = {2026},
author = {Zhang, C and Chen, J and Yang, W and Du, K and Tao, W and Lu, Q and Jiang, M and Hu, J and Zhu, Q and Elrys, AS and Cai, Z and Meng, L and Müller, C and Dan, X and Zhang, J},
title = {Small-sized biodegradable PLA microplastics inhibit plant nitrogen uptake by reshaping soil microbial communities and stimulating microbial metabolism.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143209},
doi = {10.1016/j.jhazmat.2026.143209},
pmid = {42603474},
issn = {1873-3336},
mesh = {*Polyesters/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Microplastics/toxicity ; *Microbiota/drug effects ; Bacteria/metabolism/drug effects ; *Soil Pollutants/toxicity ; *Plants/metabolism ; Particle Size ; Biodegradation, Environmental ; },
abstract = {The effects of microplastics (MPs) varying in polymer type and size on soil microbial community composition, metabolic functions, and nutrient cycling remain insufficiently understood. Here, we conducted a pot experiment using MPs differing in polymer type (non-biodegradable polyethylene [PE], and biodegradable polylactic acid [PLA]) and four particle sizes (1200-1400, 600-700, 120-150, and 25-38 μm), with amplicon sequencing, shotgun metagenomics, and nitrogen-15 ([15]N) tracing model. Our results showed that small-sized PLA-MPs (25-38 μm) reduced bacterial diversity, destabilized microbial networks, and shifted community assembly toward deterministic processes, whereas PE-MPs and larger-sized PLA-MPs exerted minimal effects. This shift was associated with enhanced depolymerization-related enzymatic potential, accompanied by greater dissolved organic carbon (DOC) availability. The resulting increase in C availability stimulated central C metabolism, promoting microbial resource acquisition and biomass synthesis. To maintain microbial C:N homeostasis, microbial N assimilation was stimulated through ammonium (NH4[+]) assimilation mediated by the glutamate dehydrogenase (GDH) and glutamine synthetase-glutamate synthase (GS-GOGAT) pathways and nitrate (NO3[-]) assimilation via assimilatory nitrate reduction to ammonium (ANRA). Consistently, the [15]N tracing model revealed that microbial assimilation rates of NH4[+]-N and NO3[-]-N increased by 10.5-fold and 12.7-fold, respectively, exceeding gross N mineralization rates, thereby depleting soil inorganic N pools and suppressing plant N uptake. Overall, our findings provide mechanistic insights into how PLA-MPs reshape soil functioning by reprogramming microbial communities and metabolism, thereby altering plant-microbe competition for N. These results highlight the potential risks of increasing biodegradable plastic inputs for cropland nutrient cycling and plant N acquisition.},
}

*Polyesters/toxicity
*Soil Microbiology
*Nitrogen/metabolism
*Microplastics/toxicity
*Microbiota/drug effects
Bacteria/metabolism/drug effects
*Soil Pollutants/toxicity
*Plants/metabolism
Particle Size
Biodegradation, Environmental

@article {pmid42623872,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {A synthetic microbiome drives a multi-omics response to remediate 1,4-dithiane-contaminated soil and simultaneously suppresses antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143337},
doi = {10.1016/j.jhazmat.2026.143337},
pmid = {42623872},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; *Microbiota ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Multiomics ; Genes, Bacterial ; },
abstract = {1,4-Dithiane, a degradation product of abandoned Japanese chemical weapons, is a persistent organic pollutant with ecological risks. A synthetic microbiome (SM) was constructed through pollution stress screening and ratio optimization, consisting of Shinella sp., Alcaligenes faecalis, Sphingomonas sp., and Stenotrophomonas sp. at an optimal ratio of 1: 1: 2: 2. The SM achieved a 1,4-dithiane degradation rate of 95.2% and reduced intermediate accumulation. Soil remediation experiments showed complete pollutant removal within 60 days, along with improved soil health: reduced bioavailability of heavy metals (Cu, Zn, Cd), increased pH (6.47-6.95), elevated organic matter and enzyme activities, and decreased salinity and redox potential. Integration of ionomics, 16S sequencing, metagenomics, metabolomics, and HT-qPCR revealed that SM colonization reshaped microbial community structure, suppressed ARG-harboring bacteria (e.g., Pseudomonas), and activated core pathways (oxidative phosphorylation and glutathione metabolism), enhancing metabolic activity and oxidative stress tolerance. Consequently, the diversity, abundance, and diffusion potential of soil ARGs and mobile genetic elements were significantly reduced. These findings provide microbial solutions and a theoretical basis for concurrent organic pollution control and soil ecological risk management.},
}

*Soil Pollutants/metabolism
*Microbiota
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Biodegradation, Environmental
Multiomics
Genes, Bacterial

@article {pmid42623874,
year = {2026},
author = {Zhou, R and Ma, Z and Kou, S and Ni, Y and Huang, X and Wei, H and Jin, Q and Xu, H and Ding, Z},
title = {Microplastics as vectors for microbial pollutants: Biofilm-associated transfer of pathogens and antibiotic resistance genes in zebrafish intestine.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143329},
doi = {10.1016/j.jhazmat.2026.143329},
pmid = {42623874},
issn = {1873-3336},
mesh = {Animals ; *Biofilms ; *Zebrafish/microbiology ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects ; *Polyesters/toxicity ; Intestines/microbiology ; Polypropylenes/toxicity ; Genes, Bacterial ; Bacteria/genetics ; Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity ; },
abstract = {As composite carriers of microorganisms and pollutants, biofilm-attached microplastics (MPs) serve as potential vectors for the environmental migration and biotransmission of antibiotic resistance genes (ARGs) and pathogens. In this study, traditional polypropylene (PP) and biodegradable polylactic acid (PLA) MPs were used to investigate the interference effects of biofilms-attached MPs on gut microbiota and ARGs transmission, through a combination of laboratory biofilm cultivation, zebrafish (Danio rerio) exposure simulations, metagenomic sequencing, and metabolomic profiling. Results showed that MP biofilms likely induced gut dysbiosis and were associated with altered diversity and abundance of pathogens and ARGs. At the phylum level, Nitrospira was transferred from PP biofilms to the gut. At the genus level, 23 genera were transferred from MP biofilms, with PLA (23 genera) showing higher transfer capacity than PP (4 genera). Notably, two human pathogens, one opportunistic pathogen, and two ARGs (adeF and oqxB) were specifically transferred from PLA biofilms, highlighting the unique dissemination risk of biodegradable MPs. Mechanistically, MPs may activate mobile genetic elements (e.g., Tn916 transposon) through metabolic remodeling and quorum sensing, thereby promoting horizontal gene transfer and ARGs dissemination within the gut. Our findings highlight the potential role of MPs as carriers of microorganisms and ARGs, underscoring the biotransmission risks of antibiotic resistance caused by composite pollution.},
}

Animals
*Biofilms
*Zebrafish/microbiology
*Microplastics/toxicity
*Drug Resistance, Microbial/genetics
*Gastrointestinal Microbiome/drug effects
*Polyesters/toxicity
Intestines/microbiology
Polypropylenes/toxicity
Genes, Bacterial
Bacteria/genetics
Gene Transfer, Horizontal
*Water Pollutants, Chemical/toxicity

@article {pmid42624114,
year = {2026},
author = {Jang, LG and Huh, JW and Kim, S and Lee, JY and Hwang, HS and Yoon, J and Lee, HG and Kim, TI and Lee, YC and Jee, SH and Kim, JF},
title = {Mouth-to-gut microbial transmission signatures enable robust, non-invasive diagnosis of gastrointestinal cancers.},
journal = {Cell host & microbe},
volume = {34},
number = {9},
pages = {1829-1842.e5},
doi = {10.1016/j.chom.2026.07.007},
pmid = {42624114},
issn = {1934-6069},
mesh = {Humans ; *Mouth/microbiology ; Feces/microbiology ; *Gastrointestinal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Middle Aged ; *Microbiota ; },
abstract = {The human microbiome is spatially compartmentalized, yet oral bacteria can ectopically colonize distal sites such as the gut, potentially influencing disease. By analyzing paired oral and fecal microbiomes from 507 participants across healthy controls and patients with metabolic disorders or gastrointestinal cancers, we established a quantitative mouth-to-feces (MF) index to measure MF microbial transmission. The MF index revealed elevated mouth-to-gut transmission in cancer and a strong association with host metabolic and inflammatory indicators. Using transmitted taxa, we developed a random forest classifier that accurately distinguished gastric/colorectal cancer from healthy controls across seven independent cohorts, even when trained solely on oral microbiome data. When benchmarked against the conventional screening test, the MF-based model achieved markedly higher sensitivity than the fecal occult blood test. These findings uncover disease-specific transmission signatures and highlight MF microbial profiling as a generalizable, non-invasive framework for gastrointestinal cancer diagnosis and risk stratification.},
}

Humans
*Mouth/microbiology
Feces/microbiology
*Gastrointestinal Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Male
Middle Aged
*Microbiota

@article {pmid42648293,
year = {2026},
author = {Oka, A and Bongers, G and Mishima, Y and Baltus, AJ and Gray, SM and Liu, B and Herzog, JW and Benedetto, JR and Fan, TJ and Jang, J and Awoniyi, M and Rousta, E and Hao, LY and Gharaibeh, RZ and Fodor, AA and Ohkusa, T and Atarashi, K and Fukuda, S and Honda, K and San Mateo, LR and Sartor, RB},
title = {Defined human Clostridia consortia reverse colitis via dual effects of tryptophan metabolites on microbiota and immunity.},
journal = {Cell host & microbe},
volume = {34},
number = {9},
pages = {1746-1763.e15},
doi = {10.1016/j.chom.2026.08.003},
pmid = {42648293},
issn = {1934-6069},
support = {K08 DK144596/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Colitis/therapy/microbiology/immunology ; *Tryptophan/metabolism ; Inflammatory Bowel Diseases/therapy/microbiology/immunology ; Mice ; Disease Models, Animal ; Dysbiosis/therapy ; Receptors, Aryl Hydrocarbon/metabolism ; *Clostridium/metabolism ; Interleukin-10/metabolism ; T-Lymphocytes, Regulatory/immunology ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; },
abstract = {Microbial dysbiosis and disrupted mucosal immune homeostasis are integrally involved in the pathogenesis of inflammatory bowel diseases (IBDs). Live biotherapeutic products (LBPs) offer a potential therapeutic strategy to restore beneficial microbes and mitigate disease. We investigated the therapeutic efficacy of 2 LBPs, human Clostridia consortia 17-mix and 11-mix, by treating established colitis in murine models. Both LBPs exhibited therapeutic effects in T cell-mediated chronic colitis models induced by human microbiota and in pathobiont-driven gnotobiotic colitis models established with combinations of IBD-relevant human-derived strains. Metagenomic and metabolomic analyses elucidated mechanisms that go beyond established functions driven by short-chain fatty acids (SCFAs) and interleukin (IL)-10-producing regulatory T cells. Notably, LBPs exerted therapeutic effects by directly inhibiting resident pathobionts and through IL-10-independent activation of host anti-inflammatory aryl hydrocarbon receptor (AhR) pathways by bacterial tryptophan metabolites. These results elucidate SCFA- and IL-10-independent protective mechanisms exerted by defined resident bacterial strains that are depleted in IBD dysbiosis.},
}

Animals
Humans
*Colitis/therapy/microbiology/immunology
*Tryptophan/metabolism
Inflammatory Bowel Diseases/therapy/microbiology/immunology
Mice
Disease Models, Animal
Dysbiosis/therapy
Receptors, Aryl Hydrocarbon/metabolism
*Clostridium/metabolism
Interleukin-10/metabolism
T-Lymphocytes, Regulatory/immunology
*Microbiota
Fatty Acids, Volatile/metabolism
Mice, Inbred C57BL
*Gastrointestinal Microbiome

@article {pmid42711823,
year = {2026},
author = {Saragiotto, GK and de Oliveira, LFV and Geciana Tomaz Dos Santos, B and Nunes Sanches, R and Merizzi de Oliveira, M and Campos Freire, F and Dias de Oliveira Carvalho, R and Sivieri, K and Sartoratto, A and Cabral, L and Azevedo, V and Belli, T and Costa Antunes, AE},
title = {Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2725874},
doi = {10.1080/15502783.2026.2725874},
pmid = {42711823},
issn = {1550-2783},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Feces/chemistry/microbiology ; *Adiposity/physiology ; *Obesity/microbiology/physiopathology ; *Marathon Running/physiology ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Body Mass Index ; *Physical Endurance/physiology ; *Running/physiology ; },
abstract = {Understanding variations in gut microbial functional potential among endurance athletes may inform future personalized nutritional strategies. This exploratory case-comparison study aimed to investigate predicted microbial functional potential using shotgun metagenomic sequencing and fecal metabolites, in two post hoc-selected runners who represented extreme and contrasting outcomes from the same single-stage 217 km mountain ultramarathon: a normal-BMI fast-finisher and an obese slow-finisher. The main descriptive findings suggest that the normal-BMI fast finisher exhibited smaller observed differences among the analyzed enzyme-coding functions and pathways in the sample collected after race completion, with a predominance of enzyme-coding functions associated with nucleic acid-related processes and protein biosynthesis. In contrast, the obese slow-finisher showed larger observed differences in predicted functional potential between the pre- and post-race samples. Distinct fecal metabolite patterns were also observed, with selective short-chain fatty acid (SCFA) changes in the normal-BMI fast-finisher and reductions across all analyzed SCFAs in the obese slow finisher. Given the limitations of this study, including the confounding effects of adiposity, unmeasured dietary intake, and post hoc selection bias, these descriptive observations provide hypothesis-generating data rather than establishing causal relationships with performance. Taken together, these findings encourage further investigation in larger cohorts.},
}

Humans
*Gastrointestinal Microbiome/physiology
Feces/chemistry/microbiology
*Adiposity/physiology
*Obesity/microbiology/physiopathology
*Marathon Running/physiology
Fatty Acids, Volatile/analysis/metabolism
Male
Body Mass Index
*Physical Endurance/physiology
*Running/physiology

@article {pmid42711968,
year = {2026},
author = {Liang, G and Wang, C and Liu, R and Ji, Q and Zhang, X and Zhao, L and Liu, X and Zhang, H and Zhuang, G and Zheng, J},
title = {Assembly Dynamics and Functional Divergence of Anaerobic Communities Driven by Iron Oxides.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70412},
doi = {10.1111/1462-2920.70412},
pmid = {42711968},
issn = {1462-2920},
support = {GYY-NYHJ-2023-WT-002//the Weiqiao-UCAS Innovation Research Projects on Carbon Neutrality Technology/ ; },
mesh = {*Ferric Compounds/metabolism/chemistry ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Sewage/microbiology ; Anaerobiosis ; Minerals/metabolism ; Ferrosoferric Oxide/metabolism ; Methane/metabolism ; Iron Compounds ; },
abstract = {Iron oxides play an important role in regulating global biogeochemical cycles, yet how their physicochemical properties influence community structure, function, and assembly remains poorly understood. Here, we investigated the effects of four representative iron oxides-ferrihydrite (Fh), goethite (Gt), haematite (Ht), and magnetite (Mt)-serving as terminal electron acceptors on microbial communities enriched from activated sludge. Metagenomic profiling revealed mineral-dependent divergence in community composition and functional potential. The communities developed on amorphous Fh demonstrated low microbial diversity and were heavily dominated by Pseudomonas_A. In contrast, the communities associated with crystalline oxides (Gt and Ht) maintained intermediate diversity. Notably, the Mt. communities exhibited a more polycentric structure, possessing the highest richness and evenness, alongside a significant enrichment of Geobacter. Methane was detected in crystalline-oxide systems but remained below detection in Fh systems. Mineralogical analyses revealed substantial Fe(III) reduction and secondary mineral formation across treatments. Null-model analysis of pairwise turnover supports mineral-associated community turnover while highlighting that the relative contributions of selection versus undominated processes vary among minerals. Overall, these findings demonstrate that iron oxide identity is associated with differences in anaerobic community structure and biogeochemical outcomes.},
}

*Ferric Compounds/metabolism/chemistry
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Sewage/microbiology
Anaerobiosis
Minerals/metabolism
Ferrosoferric Oxide/metabolism
Methane/metabolism
Iron Compounds

@article {pmid42711992,
year = {2026},
author = {Farese, M and Moraitou, M and Jin, C and Forsythe, A and Micarelli, I and van der Valk, T and Manzi, G and Parducci, L and Tafuri, MA and Guschanski, K},
title = {Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70357},
doi = {10.1002/ajpa.70357},
pmid = {42711992},
issn = {2692-7691},
support = {//Bertil Lundman Foundation for Anthropological Studies (Swedish Phytogeographical Society)/ ; DOT1326JZS//Italian Ministry of University and Research (MUR)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Italy ; History, Ancient ; *Life Style/history ; Dental Calculus/microbiology ; DNA, Ancient/analysis ; *Mouth/microbiology ; Roman World/history ; },
abstract = {OBJECTIVES: The fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social élite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall.

MATERIAL AND METHODS: We analyzed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries (I-III century CE, Lucus Feroniae and Isola Sacra) and one post-Classical cemetery (IV-VIII century CE, Selvicciola), all located in proximity to the city of Rome, Italy.

RESULTS: We detect significant differences in the taxonomic and functional composition of the oral microbiome between the three sites, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible.

DISCUSSION: The distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices, in line with previously published isotopic and morphological data. Its rural position may have mitigated the cyclical food crises that affected the contemporary Isola Sacra and the later community of Selvicciola, buffering it against the nutritional stress observed in these two locations. This finding supports the temporal stability of the dental calculus microbiome while highlighting the impact of lifestyle on the oral microbial communities.},
}

Humans
*Microbiota/genetics
Italy
History, Ancient
*Life Style/history
Dental Calculus/microbiology
DNA, Ancient/analysis
*Mouth/microbiology
Roman World/history

@article {pmid42712102,
year = {2026},
author = {Pellegrini, C and Ravaioli, F and De Fanti, S and Siliquini, A and Sala, C and Rochat, M and Pollarini, V and Polischi, B and Pasti, A and Grasso, M and Rambaldi, M and Cardoni, F and Grotteschi, N and Caraci, F and Cortelli, P and Provini, F and Lodi, R and Morandi, L and Parchi, P and Pirazzoli, GL and Sambati, L and Tonon, C and Bacalini, MG},
title = {Alterations of gut microbiota in Down syndrome and their association with Alzheimer's disease.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {9},
pages = {e71815},
doi = {10.1002/alz.71815},
pmid = {42712102},
issn = {1552-5279},
support = {PNC0000002//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; B53C22006330001//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; GR-2019-12369983-Theory-enhancing//Italian Ministry of Health/ ; //Italian Ministry of Health - "Ricerca Corrente" funding/ ; },
mesh = {Humans ; *Down Syndrome/microbiology/blood/complications ; *Alzheimer Disease/blood/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Aged ; Adult ; Biomarkers/blood ; Aged, 80 and over ; tau Proteins/blood ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Neurofilament Proteins/blood ; Glial Fibrillary Acidic Protein/blood ; },
abstract = {INTRODUCTION: Adults with Down syndrome (DS) have a higher risk of Alzheimer's disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS.

METHODS: Fecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing, filtering low prevalent taxa. Major neurocognitive disorder (NcD) was diagnosed with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria. Plasma levels of phosphorylated tau 181 (p-tau181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were measured using Simoa.

RESULTS: DS showed no changes in overall microbial diversity compared to CTRL, but genera including UBA1819 and Intestinibacter were altered. Specific genera showed changes in DS with NcD, like Alistipes (increased) and Roseburia (decreased), with the latter negatively associated with plasma AD biomarkers.

DISCUSSION: Adults with DS display AD-associated changes in GM partially resembling those reported previously in euploid AD patients.},
}

Humans
*Down Syndrome/microbiology/blood/complications
*Alzheimer Disease/blood/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
Aged
Adult
Biomarkers/blood
Aged, 80 and over
tau Proteins/blood
Feces/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Neurofilament Proteins/blood
Glial Fibrillary Acidic Protein/blood

@article {pmid42712939,
year = {2026},
author = {Tiwari, SK and Telatin, A and Singh, D},
title = {Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag110},
pmid = {42712939},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Molecular Sequence Annotation ; },
abstract = {Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.},
}

Humans
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Molecular Sequence Annotation

@article {pmid42713785,
year = {2026},
author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A},
title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70416},
doi = {10.1002/mbo3.70416},
pmid = {42713785},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Tea/microbiology
Metagenomics
Sequence Analysis, DNA
Biodiversity
Phylogeny
DNA, Bacterial/genetics/chemistry
China
DNA, Fungal/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42715940,
year = {2026},
author = {Jin, CH and Liu, SR and Song, WT and Yuan, SK and Zhang, YZ and Wang, P and Sun, XT and Liu, XQ and Fang, GY},
title = {Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {35},
pages = {27821-27839},
doi = {10.1021/acs.jafc.6c10005},
pmid = {42715940},
issn = {1520-5118},
support = {32401323//National Natural Science Foundation of China/ ; 2024LFR050//Zhejiang A and F University/ ; 2026R412A027//Xinmiao Talent Program/ ; NA//Zhejiang Provincial College Students' Science & Technology Activity Plan/ ; },
mesh = {*Acetic Acid/metabolism/chemistry ; Fermentation ; Acetobacter/genetics/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Flavoring Agents/metabolism/chemistry ; *Fungi/genetics/metabolism/classification/isolation & purification ; Saccharomyces cerevisiae/metabolism/genetics ; Metagenomics ; Microbiota ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.},
}

*Acetic Acid/metabolism/chemistry
Fermentation
Acetobacter/genetics/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
*Flavoring Agents/metabolism/chemistry
*Fungi/genetics/metabolism/classification/isolation & purification
Saccharomyces cerevisiae/metabolism/genetics
Metagenomics
Microbiota
Bacterial Proteins/genetics/metabolism

@article {pmid42200417,
year = {2026},
author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X},
title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.},
journal = {Insect molecular biology},
volume = {35},
number = {5},
pages = {489-503},
doi = {10.1111/imb.70046},
pmid = {42200417},
issn = {1365-2583},
support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Diptera/microbiology/growth & development ; Metagenomics ; Larva/microbiology/growth & development ; *Vitamin B 6/metabolism ; Symbiosis ; *Gastrointestinal Microbiome ; },
abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.},
}

Animals
*Diptera/microbiology/growth & development
Metagenomics
Larva/microbiology/growth & development
*Vitamin B 6/metabolism
Symbiosis
*Gastrointestinal Microbiome

@article {pmid42442593,
year = {2027},
author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W},
title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {592},
number = {},
pages = {121232},
doi = {10.1016/j.cca.2026.121232},
pmid = {42442593},
issn = {1873-3492},
mesh = {Humans ; *Microbiota/immunology ; *Amino Acids/metabolism ; Male ; Multiomics ; Female ; *Respiratory Tract Infections/diagnosis/immunology/metabolism/microbiology ; Aged ; *Lung/microbiology/metabolism/immunology ; Prospective Studies ; Cytokines/metabolism ; Aged, 80 and over ; Metabolomics ; },
abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.},
}

Humans
*Microbiota/immunology
*Amino Acids/metabolism
Male
Multiomics
Female
*Respiratory Tract Infections/diagnosis/immunology/metabolism/microbiology
Aged
*Lung/microbiology/metabolism/immunology
Prospective Studies
Cytokines/metabolism
Aged, 80 and over
Metabolomics

@article {pmid42706263,
year = {2026},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42706263},
issn = {2041-1723},
support = {INV-050353//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; K24AI134990//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Yang Biomedical Scholar award//UNC | University of North Carolina at Chapel Hill (UNC-Chapel Hill)/ ; },
mesh = {Animals ; *Aedes/virology ; *Dengue Virus/genetics/isolation & purification ; Humans ; Angola/epidemiology ; *Dengue/transmission/epidemiology/virology ; *Virome/genetics ; *Mosquito Vectors/virology ; Democratic Republic of the Congo/epidemiology ; Female ; Congo ; },
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collect Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirm high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

Animals
*Aedes/virology
*Dengue Virus/genetics/isolation & purification
Humans
Angola/epidemiology
*Dengue/transmission/epidemiology/virology
*Virome/genetics
*Mosquito Vectors/virology
Democratic Republic of the Congo/epidemiology
Female
Congo

@article {pmid42706609,
year = {2026},
author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX},
title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728506},
doi = {10.1080/21505594.2026.2728506},
pmid = {42706609},
issn = {2150-5608},
mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; },
abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.},
}

Animals
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Deer/microbiology/virology
Metagenome
Interspersed Repetitive Sequences
Virulence Factors/genetics
Plasmids/genetics
Bacteriophages/genetics
Virome
Bacteria/genetics/drug effects/classification
Agriculture

@article {pmid42706715,
year = {2026},
author = {Sahil, R and Jain, M},
title = {Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70197},
doi = {10.1111/1755-0998.70197},
pmid = {42706715},
issn = {1755-0998},
support = {BT/PR40261/BTIS/137/55/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Microbiota ; *Metagenomics/methods/standards ; *Plants/microbiology ; Benchmarking ; *Computational Biology/methods ; Metagenome ; },
abstract = {Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.},
}

*Microbiota
*Metagenomics/methods/standards
*Plants/microbiology
Benchmarking
*Computational Biology/methods
Metagenome

@article {pmid42707963,
year = {2026},
author = {Babu, P and Prakash, V and Subhash, S and Vanuopadath, M and Haripriyan, J and Rajan, K and Geetha, AA and P, S and Kumar, GB and Nair, BG and Madhavan, A},
title = {Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905445},
pmid = {42707963},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/immunology/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; *Immunomodulation ; },
abstract = {The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host-microbiota-pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)-Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.},
}

Humans
*Dysbiosis/immunology/therapy/microbiology
Animals
*Gastrointestinal Microbiome/immunology
Host-Pathogen Interactions/immunology
*Immunomodulation

@article {pmid42707980,
year = {2026},
author = {Li, ZL and Qu, RN and Liu, SX and Wang, W},
title = {Research progress and clinical translation prospects of the urinary tract microbiome in prostate cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1911969},
pmid = {42707980},
issn = {1664-3224},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/immunology ; *Microbiota ; *Urinary Tract/microbiology ; Translational Research, Biomedical ; Tumor Microenvironment ; Animals ; },
abstract = {Prostate cancer (PCa) is one of the most common malignancies in men worldwide, and its development is influenced by multiple factors, including genetic susceptibility, hormonal dysregulation, chronic inflammation, immune dysregulation, and remodeling of the tumor microenvironment. In recent years, the urinary tract microbiome has emerged as an important component of the tumor ecosystem and has attracted increasing attention in PCa research. Accumulating evidence indicates that patients with PCa exhibit characteristic microbial alterations in urine, expressed prostatic secretions, semen, and prostate tissue, and that certain taxa are associated with tumor grade, stage, and recurrence risk. These microbes may participate in tumor initiation and progression through a variety of mechanisms, such as inducing chronic inflammation, activating signaling pathways including TLR/NF-κB and STAT3, modulating the Treg/Th17 balance, influencing macrophage polarization, and interfering with androgen metabolism. Meanwhile, advances in 16S rRNA sequencing, metagenomics, metatranscriptomics, and multi-omics integration have provided powerful tools for characterizing host-microbe interactions and their functional relevance. In addition, microbiome-based biomarkers derived from non-invasive samples such as urine, together with artificial intelligence and causal inference approaches applied to multi-cohort data, may offer promising opportunities for early screening, risk stratification, treatment monitoring, and personalized intervention in PCa. However, current evidence remains largely associative, and the causal relationship between microbial changes and PCa has not yet been fully established. Major challenges, including contamination in low-biomass samples and inter-cohort heterogeneity, continue to hinder clinical translation. Future research should focus on longitudinal cohort studies, multicenter validation, standardized sampling workflows, and mechanistic experiments to clarify key microbial signatures and their biological functions, thereby accelerating the clinical application of the urinary tract microbiome in precision diagnosis and treatment of PCa.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/immunology
*Microbiota
*Urinary Tract/microbiology
Translational Research, Biomedical
Tumor Microenvironment
Animals

@article {pmid42708949,
year = {2026},
author = {Jiang, Y and Chen, L and Dong, H and Li, Q and Zhao, W and Zhu, F and Jiang, J and Zhang, Y and Huang, S and Xue, S},
title = {Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24764-24775},
doi = {10.1021/acs.est.5c18355},
pmid = {42708949},
issn = {1520-5851},
support = {42030711//National Natural Science Foundation of China (NSFC)/ ; 42477437//National Natural Science Foundation of China (NSFC)/ ; 42671661//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil/chemistry ; *Microbiota ; *Dissolved Organic Matter ; Soil Microbiology ; Aluminum Oxide ; Carbon ; },
abstract = {Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.},
}

*Soil/chemistry
*Microbiota
*Dissolved Organic Matter
Soil Microbiology
Aluminum Oxide
Carbon

@article {pmid42708953,
year = {2026},
author = {Francescato, L and Ghiotto, G and Valerin, MC and De Bernardini, N and Fraulini, S and Sandon, A and Treu, L and Lavagnolo, MC and Campanaro, S},
title = {Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24776-24791},
doi = {10.1021/acs.est.6c05759},
pmid = {42708953},
issn = {1520-5851},
mesh = {*Ammonia ; *Microbiota ; Anaerobiosis ; Methane/metabolism ; },
abstract = {Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.},
}

*Ammonia
*Microbiota
Anaerobiosis
Methane/metabolism

@article {pmid42236734,
year = {2026},
author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L},
title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42236734},
issn = {2052-4463},
support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Wetlands ; *Microbiota ; *Metadata ; *Metagenome ; Metagenomics ; },
abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.},
}

*Wetlands
*Microbiota
*Metadata
*Metagenome
Metagenomics

@article {pmid42315898,
year = {2026},
author = {Mishra, S and Mutnuri, S},
title = {Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42315898},
issn = {2045-2322},
mesh = {*Fermentation ; *Metagenomics/methods ; Arctic Regions ; *Hydrogen/metabolism ; Kinetics ; Microbiota ; *Biofuels ; *Ice ; },
abstract = {Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.},
}

*Fermentation
*Metagenomics/methods
Arctic Regions
*Hydrogen/metabolism
Kinetics
Microbiota
*Biofuels
*Ice

@article {pmid42332773,
year = {2026},
author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q},
title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.},
journal = {BMC medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42332773},
issn = {1741-7015},
support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Imidazoles/blood ; *Dietary Fiber/administration & dosage ; *Coronary Disease/blood/epidemiology/microbiology ; *Histidine/administration & dosage/metabolism ; Middle Aged ; Prospective Studies ; *Propionates/blood ; Adult ; },
abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.

METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.

RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles = 1.82; 95%CI = 1.17-2.81; p-trend = 0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction = 0.01). Similar interactions were seen for total fiber (p = 0.09), soluble fiber (p = 0.09), and insoluble fiber (p = 0.11), without statistical significance.

CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.},
}

Humans
*Gastrointestinal Microbiome
Male
*Imidazoles/blood
*Dietary Fiber/administration & dosage
*Coronary Disease/blood/epidemiology/microbiology
*Histidine/administration & dosage/metabolism
Middle Aged
Prospective Studies
*Propionates/blood
Adult

@article {pmid42508343,
year = {2026},
author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK},
title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.},
journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine},
volume = {237},
number = {},
pages = {112830},
doi = {10.1016/j.apradiso.2026.112830},
pmid = {42508343},
issn = {1872-9800},
mesh = {Animals ; Male ; *Gamma Rays ; *Spodoptera/microbiology/radiation effects ; *Gastrointestinal Microbiome/radiation effects ; Bacteria/radiation effects/genetics ; },
abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.},
}

Animals
Male
*Gamma Rays
*Spodoptera/microbiology/radiation effects
*Gastrointestinal Microbiome/radiation effects
Bacteria/radiation effects/genetics

@article {pmid42518032,
year = {2026},
author = {Li, F and Zhao, H and Lei, Y and Luo, J and Chen, B and Li, C and Zhao, X and Jiang, H},
title = {Fufangteng Yixin Formula alleviates myocardial ischemia-reperfusion injury by modulating gut microbiota and resultant metabolites in rats.},
journal = {Journal of natural medicines},
volume = {80},
number = {5},
pages = {1521-1537},
pmid = {42518032},
issn = {1861-0293},
support = {2024GXNSFBA010207//Guangxi Natural Science Foundation Joint Special Project/ ; },
mesh = {Animals ; Rats ; *Myocardial Reperfusion Injury/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats, Wistar ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; },
abstract = {This study aimed to explore whether Fufangteng Yixin Formula (FFTYXF) can ameliorate myocardial ischemia-reperfusion injury (MIRI) by regulating the gut microbiota and resultant metabolites. Wistar rats were given FFTYXF by gavage for 7 days, and MIRI rat model was established. Serum level of inflammatory markers was determined by ELISA, and heart function was evaluated by echocardiography. Myocardial histological changes and infarct size were examined by hematoxylin-eosin and triphenyltetrazolium chloride staining, respectively. 16S rRNA gene and metagenomics analyses were employed to explore gut microbiota, while untargeted metabolomics analysis was used to explore serum metabolites. FFTYXF pretreatment could significantly improve cardiac function, reduce infarct size, decrease level of inflammatory factors (TNF-α and IL-6) and inflammatory cells infiltration. At genus level, g__Oscillibacter and g__Rikenellaceae_RC9_gut_group were identified as key microbial bacteria in MIRI rat response to FFTYXF pretreatment. After FFTYXF pretreatment, the functional categories of gut microbiota were participated in fatty acid (FA) biosynthesis/metabolism, glycolysis _ gluconeogenesis and sphingolipid metabolism. Genes response to FFTYXF pretreatment in MIRI rats included K00023 (phbB), K00281 (GLDC, gcvP), K03879 (ND2), K07827 (KRAS) and K15192 (BTAF1), and they were mainly participated in carbon, butanoate, glyoxylate and dicarboxylate metabolism. Differential metabolites were also mainly participated in FA biosynthesis/metabolism, such as alpha-Linolenic acid, omega-3/omega-6 FA, and flavan-3-ol metabolic pathway. Abundance of g__Rikenellaceae_RC9_gut_group positively correlated with differential metabolites FAHFA 34:0, FAHFA 16:1/18:3, and FA 24:5. FFTYXF could alleviate MIRI by modulating gut microbial bacteria alteration and resultant metabolites, particularly short-chain FAs.},
}

Animals
Rats
*Myocardial Reperfusion Injury/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects
Male
Rats, Wistar
*Drugs, Chinese Herbal/pharmacology/therapeutic use

@article {pmid42631636,
year = {2026},
author = {Azouz, S and Benabid, M and Zarrouk, S and Elati, J and Aoun, K and Bouratbine, A},
title = {Contribution of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) to the characterization of the gut microbiota in Tunisia, North Africa.},
journal = {FEMS microbiology letters},
volume = {373},
number = {},
pages = {},
doi = {10.1093/femsle/fnag095},
pmid = {42631636},
issn = {1574-6968},
support = {//Ministry of Higher Education and Science/ ; },
mesh = {Humans ; Tunisia ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Pilot Projects ; Adult ; Metagenomics/methods ; Metagenome ; Shotgun Sequencing ; Male ; Female ; },
abstract = {This pilot study aimed to assess the enhanced capabilities of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) for identifying specific microbiota patterns in healthy adults in Tunisia. Shotgun metagenomic sequencing was performed on 21 stool samples. Taxonomic classification was carried out using Kraken2, followed by Bracken analysis. Enterotype (ET) assignment was performed using a publicly available, reference-based classification tool involving Fuzzy-k-means (FKM) clustering. Next, NMF was applied to identify 'enterosignatures' (ESs). The FKM approach revealed a co-dominance of Prevotella-ET (P-ET, 57%) and Firmicutes-ET (F-ET, 38%) with 41% of P-ET samples exhibiting a significant deviation from the reference enterotype center. These latter had a lower proportion of Prevotella-ES and a higher proportion of Bacteroides/Phocaeicola-, Firmicutes- and/or Bifidobacterium-enriched ESs. The F-ET samples were differentially enriched by Blautia (P = 0.007) and Vescimonas (P = 0.007). NMF revealed within this group, a candidate Firmicutes-associated ES driven by Blautia and encompassing Vescimonas, Akkermansia, and Methanobrevibacter. These findings demonstrate the combined power of refined enterotyping and NMF in characterizing gut microbiota, providing a key methodology for future large-scale research. However, our relatively small sample size limits statistical power and biological interpretation, making this study exploratory in nature. Candidate ES requires validation in larger independent datasets.},
}

Humans
Tunisia
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Pilot Projects
Adult
Metagenomics/methods
Metagenome
Shotgun Sequencing
Male
Female

@article {pmid42641809,
year = {2026},
author = {Wang, J and Zhang, D and Hu, S and Guo, H and Zou, L and Wang, N and Xie, J and Wang, Z and Hao, M and Da, Y and Wang, M and Song, L and Li, H and Sun, B},
title = {Limosilactobacillus reuteri and Lactobacillus johnsonii intervention ameliorates gestational diabetes mellitus-associated sex-specific placental nutrient transporter abnormalities: Links with tryptophan metabolism and aryl hydrocarbon receptor signaling.},
journal = {Diabetes research and clinical practice},
volume = {240},
number = {},
pages = {113510},
doi = {10.1016/j.diabres.2026.113510},
pmid = {42641809},
issn = {1872-8227},
mesh = {Female ; Pregnancy ; Animals ; *Limosilactobacillus reuteri/physiology ; *Diabetes, Gestational/metabolism/microbiology/therapy ; Humans ; *Placenta/metabolism ; Mice ; *Tryptophan/metabolism ; *Probiotics/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction ; *Lactobacillus johnsonii ; Male ; Adult ; Gastrointestinal Microbiome ; },
abstract = {AIMS: Gestational diabetes mellitus (GDM) is a common pregnancy complication associated with maternal metabolic abnormalities and adverse offspring outcomes. Although GDM is closely linked to gut microbiota dysbiosis, key probiotic strains and underlying mechanisms remain unclear. This study aimed to identify potential probiotics using microbial signals from clinical GDM cases and a mouse model.

METHODS: Metagenomic sequencing was performed on fecal samples from normal and GDM pregnant women; a GDM mouse model was then established for candidate probiotic screening. Combined intervention with Limosilactobacillus reuteri and Lactobacillus johnsonii was applied to assess glucose metabolism, inflammation, intestinal barrier, placental structure, nutrient transporter expression and tryptophan metabolism.

RESULTS: Metagenomic analysis showed reduced Lactobacillaceae in GDM women, and the two strains were identified as candidates. The intervention improved glycemic control, insulin resistance, inflammation and colon barrier function, and alleviated placental lesions. Placental nutrient transporters expression showed sex-specific abnormalities that were normalized by probiotics. Maternal plasma 5-hydroxyindoleacetic acid (5-HIAA) was reduced in GDM mice and restored after intervention, correlating with metabolic indices, placental status, fetal growth and aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: Combined L. reuteri and L. johnsonii intervention improved GDM-associated maternal metabolic and sex-specific placental abnormalities.},
}

Female
Pregnancy
Animals
*Limosilactobacillus reuteri/physiology
*Diabetes, Gestational/metabolism/microbiology/therapy
Humans
*Placenta/metabolism
Mice
*Tryptophan/metabolism
*Probiotics/therapeutic use
*Receptors, Aryl Hydrocarbon/metabolism
Signal Transduction
*Lactobacillus johnsonii
Male
Adult
Gastrointestinal Microbiome

@article {pmid42702602,
year = {2026},
author = {Li, Y and Chen, T and Li, P and Zhang, G and Tian, Y and Wang, J and Ni, J},
title = {Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42702602},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Ice Cover/virology ; Tibet ; *Rivers/virology ; Altitude ; Ecosystem ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; },
abstract = {The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.},
}

*Ice Cover/virology
Tibet
*Rivers/virology
Altitude
Ecosystem
*Viruses/genetics/classification/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral

@article {pmid42702845,
year = {2026},
author = {Xue, Z and Xu, H and Zhu, L and Zhao, D},
title = {Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.},
journal = {Chemical biology & drug design},
volume = {108},
number = {3},
pages = {e70397},
doi = {10.1111/cbdd.70397},
pmid = {42702845},
issn = {1747-0285},
mesh = {Animals ; Humans ; Multiomics ; *Prevotella melaninogenica/metabolism/physiology ; *Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy ; *Mycoplasma pneumoniae ; Mice ; *Butyrates/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Disease Models, Animal ; Microbiota ; },
abstract = {Mycoplasma pneumoniae (MP) is one of the main pathogens causing atypical pneumonia in children. The susceptible population is mainly children and adolescents over 5 years old, and the infection rate has increased in recent years. At present, there is limited research on the pulmonary microbiota of patients with Mycoplasma pneumoniae pneumonia, and the characteristics of their microbiota are not yet clear. We included MPP children in stages and established two independent cohorts. Cohort I (n = 175) performed 16S rRNA sequencing on bronchoalveolar lavage fluid (BALF) to explore microbial genus level characteristics, while Cohort II (n = 41) performed metagenomic and transcriptome sequencing to explore microbial species level characteristics and predict inter group differential metabolic pathways. Finally, a murine model infected with MP was established to validate the effects of Prevotella melaninogenica and its metabolite butyrate. Based on Multi-Omic Analysis, we discovered that P. melaninogenica was the most discriminative species enriched in the critically ill group. Functional profiling demonstrated that butanoate metabolism pathways were significantly enriched in the severe group and positively correlated with P. melaninogenica abundance. Transcriptomic analysis revealed that P. melaninogenica-associated host genes were significantly enriched in immune regulation pathways. Animal experiments confirmed that both P. melaninogenica and butyrate pretreatment significantly attenuated MP-induced pulmonary inflammation, pathogen load, and immune cell infiltration. Respiratory microbiota dysbiosis may be associated with MPP severity. Prevotella melaninogenica, a potential protective commensal enriched in severe group MPP patients, may alleviate airway inflammation through its metabolite butyrate.},
}

Animals
Humans
Multiomics
*Prevotella melaninogenica/metabolism/physiology
*Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy
*Mycoplasma pneumoniae
Mice
*Butyrates/metabolism
Male
Female
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Child
Child, Preschool
Disease Models, Animal
Microbiota

@article {pmid42703994,
year = {2026},
author = {Kar, P and Halder, J and Rout, SR and Dash, P and Das, C and Ghosh, G and Rath, G and Kar, B},
title = {Marine-derived Bioactive Compounds: A Promising Frontier against Multidrug-resistant Microbial Infections.},
journal = {Mini reviews in medicinal chemistry},
volume = {26},
number = {12},
pages = {841-858},
pmid = {42703994},
issn = {1875-5607},
mesh = {Humans ; *Biological Products/chemistry/pharmacology/isolation & purification ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria/drug effects ; *Bacterial Infections/drug therapy ; Microbial Sensitivity Tests ; },
abstract = {The global escalation of Multidrug-Resistant (MDR) bacterial infections poses a serious and growing threat to public health, contributing to increased morbidity, mortality, and substantial economic burden worldwide. The widespread and often indiscriminate use of antibiotics in clinical and agricultural settings has accelerated the emergence of resistance, significantly diminishing the efficacy of conventional antimicrobial therapies. This pressing challenge necessitates the exploration of alternative sources for novel antibiotics. Marine ecosystems-renowned for their immense biodiversity and ecological complexity-have gained attention as a rich and largely untapped reservoir of bioactive natural products with potent antimicrobial activity. Marine organisms, such as sponges, tunicates, algae, and bacteria and fungi derived from marine sources, produce structurally diverse and pharmacologically active metabolites, including peptides, polyketides, alkaloids, terpenoids, sterols, lactones, and halogenated compounds. Many of these marine-derived molecules possess unique chemical scaffolds and novel mechanisms of action, offering the potential to circumvent existing resistance pathways. Some compounds have shown promising activity against MDR pathogens, including Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. However, challenges such as low natural abundance, difficulty in cultivation, and structural complexity have limited their clinical translation. Recent advancements in marine biotechnology, genomics, metagenomics, and synthetic biology have opened new avenues for the discovery, biosynthesis, and structural optimization of these compounds. These innovative approaches not only facilitate sustainable production but also enhance the pharmacological properties.},
}

Humans
*Biological Products/chemistry/pharmacology/isolation & purification
*Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification
Animals
*Aquatic Organisms/chemistry/metabolism
*Drug Resistance, Multiple, Bacterial/drug effects
Bacteria/drug effects
*Bacterial Infections/drug therapy
Microbial Sensitivity Tests

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704656,
year = {2026},
author = {Bates, KA and Rivera, VB and Glicklich, D and Diflo, T and Chaturvedi, V and Nog, R},
title = {Urinary microbiome in renal transplant patients with BK polyomavirus reactivation.},
journal = {Journal of medical microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002196},
pmid = {42704656},
issn = {1473-5644},
mesh = {Humans ; *BK Virus/physiology/genetics ; *Kidney Transplantation/adverse effects ; *Polyomavirus Infections/urine/microbiology/virology ; *Microbiota ; Male ; Female ; Middle Aged ; Adult ; *Virus Activation ; Bacteria/classification/genetics/isolation & purification ; *Tumor Virus Infections/urine/microbiology/virology ; Aged ; DNA, Viral/blood ; *Urine/microbiology ; },
abstract = {Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.},
}

Humans
*BK Virus/physiology/genetics
*Kidney Transplantation/adverse effects
*Polyomavirus Infections/urine/microbiology/virology
*Microbiota
Male
Female
Middle Aged
Adult
*Virus Activation
Bacteria/classification/genetics/isolation & purification
*Tumor Virus Infections/urine/microbiology/virology
Aged
DNA, Viral/blood
*Urine/microbiology

@article {pmid42705715,
year = {2026},
author = {Li, G and Shen, L and Nie, L and Tang, P and Shan, Q and Qin, L and Fan, S and Guo, X},
title = {Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120307},
doi = {10.1016/j.foodres.2026.120307},
pmid = {42705715},
issn = {1873-7145},
mesh = {*Fermentation ; *Volatile Organic Compounds/analysis ; *Gas Chromatography-Mass Spectrometry/methods ; *Electronic Nose ; *Metagenomics/methods ; *Microbiota ; *Food Microbiology/methods ; Taste ; Odorants/analysis ; *Edible Grain/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.},
}

*Fermentation
*Volatile Organic Compounds/analysis
*Gas Chromatography-Mass Spectrometry/methods
*Electronic Nose
*Metagenomics/methods
*Microbiota
*Food Microbiology/methods
Taste
Odorants/analysis
*Edible Grain/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Bacteria/classification/metabolism/genetics

@article {pmid42705723,
year = {2026},
author = {Tong, W and Wang, H and Yang, Y and Xu, J and Huang, Z and Huang, D and Luo, H and Zhao, L and Zhang, S},
title = {Enzyme-driven synthesis and metabolic mechanism of ferulic acid in strong-flavor Daqu: pathway elucidation and microbial drivers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120354},
doi = {10.1016/j.foodres.2026.120354},
pmid = {42705723},
issn = {1873-7145},
mesh = {*Coumaric Acids/metabolism/analysis ; Fermentation ; Carboxylic Ester Hydrolases/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism ; Carboxy-Lyases/metabolism ; Bacteria/metabolism ; Metabolic Networks and Pathways ; Microbiota ; },
abstract = {Ferulic acid (FA) is a bioactive phenolic compound in strong-flavor Baijiu with important health functions. Its microbial synthesis and metabolic mechanisms in strong-flavor Daqu remain unclear, limiting the understanding of its production. This study explored FA synthesis and metabolic dynamics during Daqu fermentation from D0-D90 using physicochemical detection, feruloyl esterases (FAEs) activity assay, and metagenomic sequencing. Results indicated that FA content fluctuated dynamically throughout fermentation, reaching a final level of 4.39 ± 0.17 mg/kg, and FAEs activity was significantly positively correlated with FA content. Genera significantly associated with FA dynamics were identified. High-abundance genera including Lichtheimia, Saccharopolyspora, Aspergillus, Byssochlamys and Rasamsonia exhibited significantly positive correlations with FA accumulation at respective fermentation stages. This phenomenon may be attributed to their capacity to secrete FAEs, thereby promoting the release of FA. The dynamic change of free FA content was also associated with the expression of ferulic acid decarboxylase, a key enzyme potentially involved in free FA degradation. A comprehensive FA metabolic network in Daqu was constructed, including the cell wall release pathway and the shikimate biosynthesis pathway. A metabolic association model was established based on the phasic succession of fungal and bacterial communities and their coupling with FA metabolic enzyme systems, which suggested a potential division of labor. Fungi are likely to participate in free FA release through secretion of FAEs and auxiliary degrading enzymes, while bacteria may mainly participate in the metabolic turnover and consumption of free FA. This study expands the current understanding of phenolic acid metabolism in strong-flavor Daqu, and provides a theoretical basis for interpreting FA metabolic characteristics during Daqu fermentation.},
}

*Coumaric Acids/metabolism/analysis
Fermentation
Carboxylic Ester Hydrolases/metabolism
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism
Carboxy-Lyases/metabolism
Bacteria/metabolism
Metabolic Networks and Pathways
Microbiota

@article {pmid42705725,
year = {2026},
author = {Xiao, L and Wan, Y and Jiang, M and Liu, Z and Chen, G and Ke, S and Jiang, J and Guo, S and Yu, P and Wu, H and Wang, A and Ning, M and Zhou, Z},
title = {Effects of extraction methodologies on structural characterization and gut microbiota fermentation properties of Apocynum venetum polysaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120357},
doi = {10.1016/j.foodres.2026.120357},
pmid = {42705725},
issn = {1873-7145},
mesh = {*Fermentation ; *Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Apocynum/chemistry ; Prebiotics ; Bacillus/metabolism ; *Plant Extracts/chemistry ; Hydrogen-Ion Concentration ; },
abstract = {Apocynum venetum L. polysaccharides are classified into neutral-to-acidic heteropolysaccharides rich in glucuronic acid, exhibiting antioxidant, immunomodulatory, and potential prebiotic activities. Different extraction methods have a significant impact on the structural characterization and biological activity of polysaccharides. This study aims to compare the structural characteristics and in vitro prebiotic activity of the Apocynum venetum L. polysaccharides BAC and CEL-U obtained via Bacillus velezensis fermentation and the combined ultrasonic-cellulase method, respectively. The results showed that BAC and CEL-U were acidic heteropolysaccharides composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, and they all showed linear branching structure. Compared with CEL-U, BAC had lower molecular weight (17.51 kDa), higher uronic acid content (27.27%) and typical triple helix structure. In vitro fermentation showed that BAC can produce more propionic acid and butyric acid, maintain a lower pH, promote the proliferation of beneficial bacteria (Segatella and Prevotella), and inhibit potentially harmful bacteria. Metagenome analysis further revealed that BAC played a prebiotic role by activating specific glycosidase-mediated degradation pathways and enriching functional pathways related to carbohydrate metabolism. These findings clarify the structure-activity relationship of Apocynum venetum polysaccharide and provide a theoretical basis for its targeted application in the field of intestinal health.},
}

*Fermentation
*Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology
*Gastrointestinal Microbiome/physiology
*Apocynum/chemistry
Prebiotics
Bacillus/metabolism
*Plant Extracts/chemistry
Hydrogen-Ion Concentration

@article {pmid42705727,
year = {2026},
author = {Xu, S and Li, J and Wang, F and Bian, H and Yan, W and Wang, H and Jiang, C and Sun, J and Wang, Z and Li, X},
title = {Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120362},
doi = {10.1016/j.foodres.2026.120362},
pmid = {42705727},
issn = {1873-7145},
mesh = {*Hydrogen/metabolism ; *Fermentation ; Bacteria/metabolism/classification/genetics ; Archaea/metabolism/genetics/classification ; *Wine/microbiology/analysis ; *Food Microbiology ; *Microbiota ; Metagenomics ; China ; *Alcoholic Beverages/microbiology ; },
abstract = {Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.},
}

*Hydrogen/metabolism
*Fermentation
Bacteria/metabolism/classification/genetics
Archaea/metabolism/genetics/classification
*Wine/microbiology/analysis
*Food Microbiology
*Microbiota
Metagenomics
China
*Alcoholic Beverages/microbiology

@article {pmid42705729,
year = {2026},
author = {Li, Y and Li, J and Deng, J and Xia, P and Zhou, G and Zhu, Z and Ding, Y and Yang, J and Zhang, F},
title = {Phocaeicola vulgatus alleviates obesity through cross-species arginine production and hepatic retinoic acid signaling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120365},
doi = {10.1016/j.foodres.2026.120365},
pmid = {42705729},
issn = {1873-7145},
mesh = {*Arginine/biosynthesis/metabolism ; Animals ; *Obesity/therapy/microbiology/metabolism ; *Liver/metabolism ; Signal Transduction ; *Tretinoin/metabolism ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Gastrointestinal Microbiome ; Diet, High-Fat ; },
abstract = {Fecal microbiota transplantation (FMT) shows inconsistent clinical efficacy in treating obesity, and the specific microbial determinants dictating its success remain poorly characterized. Our previous clinical FMT trial identified Phocaeicola vulgatus as a key microbe contributing to the therapeutic efficacy of obesity treatment. Here, to investigate its role in obesity, we established an independent clinical cohort comprising obese and lean individuals, revealing that the P. vulgatus-centered network and ornithine synthesis are impaired in the obese group. We then confirmed causality by utilizing a humanized rat model carrying microbiota from a P. vulgatus-deficient obese patient, demonstrating that P. vulgatus supplementation significantly mitigates HFD-induced obesity, including reductions in body weight and serum total cholesterol levels, as well as the alleviation of hepatic steatosis. To further explore the functional mechanisms of P. vulgatus, integrated metagenomic and metabolomic analyses revealed a potential functional association between P. vulgatus and Phascolarctobacterium faecium that is associated with enhanced intestinal arginine biosynthesis and systemic availability. Furthermore, hepatic transcriptomics linked these elevated circulating arginine levels to the upregulation of retinoic acid (RA) signaling. Taken together, our findings outline a potential microbial-host network wherein P. vulgatus mitigates obesity via the arginine-RA axis, providing a valuable scientific basis for exploring this strain as a probiotic candidate for metabolic health.},
}

*Arginine/biosynthesis/metabolism
Animals
*Obesity/therapy/microbiology/metabolism
*Liver/metabolism
Signal Transduction
*Tretinoin/metabolism
Rats
Humans
Fecal Microbiota Transplantation
Male
Gastrointestinal Microbiome
Diet, High-Fat

@article {pmid42705742,
year = {2026},
author = {Han, G and Li, K and Wang, J and Xu, P and Liu, T and Xu, X and Zhao, Y},
title = {Mechanistic insights into flavor deterioration in bitter sturgeon caviar: Evidence from lipidomics and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120381},
doi = {10.1016/j.foodres.2026.120381},
pmid = {42705742},
issn = {1873-7145},
mesh = {Animals ; *Metagenomics ; *Fishes ; *Lipidomics ; *Taste ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Microbiota ; Bacteria ; *Seafood/analysis/microbiology ; Humans ; },
abstract = {This study systematically compared the flavor and multi-omics differences between normal caviar and bitter caviar based on quantitative descriptive analysis (QDA), volatile compounds (VOCs) analysis, untargeted lipidomics, and metagenomics. The results showed that bitter caviar was characterized not only by increased bitterness, but also by decreased positive sensory attributes, including buttery, nutty, and marine fresh. VOCs analysis indicated that the volatile profile of bitter caviar was reorganized. Compounds such as 3-hydroxy-2-butanone, 1-octen-3-ol, and (E, Z)-2,6-nonadienal showed higher relative odor activity values (rOAVs); however, these changes did not improve its overall sensory experience. Untargeted lipidomics identified 492 differential lipids. These changes were mainly characterized by decreased PC and increased DG and LPC in bitter caviar. KEGG pathways analysis showed that these differential lipids were mainly associated with glycerophospholipid metabolism, choline metabolism in cancer, and retrograde endocannabinoid signaling. Metagenomic analysis showed that bacteria dominated the microbial community of caviar. Among them, Bacillus and Micromonospora showed relatively high abundance in the caviar microbiota. They were also closely associated with lipid metabolic changes involving PC, DG, and LPC, suggesting their potential as candidate targets for future microbiota-directed regulation of caviar quality. These findings provide new insights into the mechanisms underlying sensory deterioration and flavor formation in bitter caviar, and offer a theoretical basis for improving caviar quality in industrial production.},
}

Animals
*Metagenomics
*Fishes
*Lipidomics
*Taste
Volatile Organic Compounds/analysis
Odorants/analysis
Microbiota
Bacteria
*Seafood/analysis/microbiology
Humans

@article {pmid42566926,
year = {2026},
author = {Carvalho, LB and da Silva, GR and de Oliveira Franzote, VH and Larcerda-Júnior, GV and Fernandes-Júnior, PI and Oliveira, VM and Matteoli, FP},
title = {Marked dominance of Actinomycetota and compositional shifts in bacterial communities in Brazilian dryland soils under land-use change.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128660},
doi = {10.1016/j.micres.2026.128660},
pmid = {42566926},
issn = {1618-0623},
mesh = {*Soil Microbiology ; Brazil ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; Forests ; Agriculture ; Soil/chemistry ; *Actinobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; Tropical Climate ; Biodiversity ; *Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Tropical dry forests are among the most threatened and least studied tropical forest ecosystems worldwide. The Caatinga, the largest tropical dry forest in South America, comprises preserved and agriculturally impacted areas, providing a valuable model system to investigate how semiarid soil bacterial communities respond to natural seasonality and land-use change. Here, we evaluated how land-use and seasonality shape microbial community structure and ecological strategies in soils from conserved forest (CEF) and agriculture-influenced areas (BEF) across rainy and dry seasons using a contig-based taxonomy approach combined with ANCOM-BC2 differential abundance analysis and co-occurrence networks inference. A total of 74 phyla and 1015 genera were identified, with marked predominance of Actinomycetota (61.4%). Seasonal responses were mainly detected in BEF, where Trebonia and Mycobacterium were enriched during the dry season, while Solirubrobacter was more abundant in the rainy season. Taxa putatively associated with plant growth promotion and biological soil crust formation were consistently detected in both areas, whereas oligotrophic and methanotrophic groups were more enriched in CEF and taxa related to biocontrol potential were more represented in BEF. The proportion of seasonal generalists was higher in CEF than in BEF, representing 86.0% and 46.6% of the detected taxa, respectively, suggesting greater temporal stability in conserved soils. Co-occurrence networks revealed that CEF exhibited a sparser and more modular structure, whereas BEF displayed a highly interconnected network. Notably, all module hubs belonged to Actinomycetota. Together, these findings demonstrate that land-use intensification reshapes bacterial ecological strategies and network organization, reducing community heterogeneity under agricultural management.},
}

*Soil Microbiology
Brazil
Seasons
*Bacteria/classification/genetics/isolation & purification
Forests
Agriculture
Soil/chemistry
*Actinobacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
Ecosystem
Tropical Climate
Biodiversity
*Microbiota
DNA, Bacterial/genetics

@article {pmid42585836,
year = {2026},
author = {Cao, Y and Du, P and Zhai, R and Guo, Y and Lin, M and Wang, Z},
title = {Drought stress adaptation in Ficus carica L.: Modulation of ROS scavenging, nitrogen uptake, and rhizosphere bacterial community assembly and functions.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128678},
doi = {10.1016/j.micres.2026.128678},
pmid = {42585836},
issn = {1618-0623},
mesh = {*Ficus/microbiology/physiology/growth & development/metabolism ; *Nitrogen/metabolism ; *Rhizosphere ; Soil Microbiology ; *Reactive Oxygen Species/metabolism ; Drought Resistance ; *Droughts ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Nitrogen Fixation/genetics ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Photosynthesis ; Adaptation, Physiological ; },
abstract = {Rhizosphere microorganisms are crucial for plant drought resistance; however, their response to drought stress in fig plants remains poorly understood. In this study, potted 'BoJi Red' fig plants were utilized to systematically investigate drought-induced changes in the structure, assembly processes, and functional potential of rhizosphere bacterial communities. The results showed that drought significantly inhibited fig growth, photosynthesis, and nitrogen uptake, while increasing reactive oxygen species (ROS) content and antioxidant enzyme activities, although these enzyme activities declined under severe drought conditions. Bacterial community richness and diversity significantly increased under moderate and severe drought, shifting toward drought-resistant groups, notably Actinomycetota and Bacillota. The number of nodes, links, and key species in the microbial co-occurrence network decreased as drought intensified, with stochastic processes dominating community assembly. Moreover, ecological niche breadth and the proportion of generalist species increased with drought severity. Notably, Nocardioidaceae was significantly enriched under drought, and metagenomic profiling indicated this taxon is strongly associated with carbohydrate metabolism pathways, with predicted genetic potential to participate in soil carbon turnover and nutrient transformation. Additionally, drought significantly reduced the abundance of nitrogen-fixing genes (nifD, nifK) and weakened the relative contribution of Rhizobiaceae to nitrogen fixation; correlative functional profiling suggests Nocardioidaceae may possess alternative nitrogen cycling pathways that could partially offset suppressed rhizosphere nitrogen fixation capacity. Overall, these findings indicate that the fig plant response to drought stress involves both physiological adjustments in the host and functional reconfiguration of the rhizosphere microbial community, with Nocardioidaceae playing a key role in maintaining rhizosphere functions and enhancing drought tolerance.},
}

*Ficus/microbiology/physiology/growth & development/metabolism
*Nitrogen/metabolism
*Rhizosphere
Soil Microbiology
*Reactive Oxygen Species/metabolism
Drought Resistance
*Droughts
*Bacteria/classification/genetics/metabolism/isolation & purification
Nitrogen Fixation/genetics
*Stress, Physiological
Plant Roots/microbiology
Microbiota
Photosynthesis
Adaptation, Physiological

@article {pmid42636661,
year = {2026},
author = {Zeng, Y and Tao, Q and Fan, J and Wang, Y and Tao, R and Rao, J and Zeng, F and Jiang, F and Zhang, C and Xiong, X and Cheng, X},
title = {Desert-derived Ensifer sp. SA403 enhances potato salt tolerance by reshaping rhizosphere microbiome functions and host responses.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128695},
doi = {10.1016/j.micres.2026.128695},
pmid = {42636661},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Solanum tuberosum/microbiology/physiology/growth & development ; *Salt Tolerance ; Soil Microbiology ; *Microbiota ; *Rhizobiaceae/genetics/isolation & purification/physiology/classification ; Plant Roots/microbiology ; Salinity ; Host Microbial Interactions ; Desert Climate ; Metagenomics ; Sodium/metabolism ; Soil/chemistry ; },
abstract = {Soil salinization increasingly threatens global food security, and potato (Solanum tuberosum L.), a moderately salt-sensitive crop, is particularly vulnerable to saline soils. Plant growth-promoting rhizobacteria (PGPR) offer a promising strategy to improve crop performance, yet how PGPR interact with native microorganisms to enhance potato salt tolerance remains poorly understood. In this study, we identified a desert-derived PGPR strain, Ensifer sp. SA403, which substantially enhanced potato performance under high salinity across sterile, non-sterile and field conditions. Physiologically, inoculation with SA403 reduced shoot Na[+] accumulation and increased the K[+]/Na[+] ratio; notably, these effects were markedly stronger in non-sterile substrates than under sterile conditions, indicating that SA403-mediated ion homeostasis relies on cooperation with the resident microbiota rather than on the strain acting alone. Metagenomic profiling indicated that SA403 strain reshaped rhizosphere communities, significantly enriching beneficial taxa such as Priestia and Bradyrhizobium, and upregulated functional pathways involved in glutathione and sulfur metabolism. Furthermore, host transcriptomic analyses showed that SA403 modulated plant responses to salt stress, with differentially expressed genes enriched in jasmonic acid signaling, ethanolamine metabolism and amino-acid biosynthesis pathways. Field trials on saline soils confirmed that SA403 significantly increased seedling emergence and tuber weight. Together, our results demonstrate that SA403 functions as a biological mediator that optimizes rhizosphere microecology and coordinates ion balance and host signaling to enhance potato salt tolerance. These findings support the potential of SA403 as a robust PGPR-based tool for sustainable potato production on saline soils.},
}

*Rhizosphere
*Solanum tuberosum/microbiology/physiology/growth & development
*Salt Tolerance
Soil Microbiology
*Microbiota
*Rhizobiaceae/genetics/isolation & purification/physiology/classification
Plant Roots/microbiology
Salinity
Host Microbial Interactions
Desert Climate
Metagenomics
Sodium/metabolism
Soil/chemistry

@article {pmid42636663,
year = {2026},
author = {Wang, D and Huang, Z and Sun, S and Song, W and Li, Y and Sun, K and Li, Z and Feng, J},
title = {Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128696},
doi = {10.1016/j.micres.2026.128696},
pmid = {42636663},
issn = {1618-0623},
mesh = {Animals ; Multiomics ; *Soil Microbiology ; *Ascomycota/drug effects/isolation & purification ; *Caves/microbiology ; *Chiroptera/microbiology ; Metabolomics ; *Antifungal Agents/pharmacology/metabolism ; China ; Microbiota/genetics ; Metagenomics ; Soil/chemistry ; },
abstract = {White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.},
}

Animals
Multiomics
*Soil Microbiology
*Ascomycota/drug effects/isolation & purification
*Caves/microbiology
*Chiroptera/microbiology
Metabolomics
*Antifungal Agents/pharmacology/metabolism
China
Microbiota/genetics
Metagenomics
Soil/chemistry

@article {pmid42420833,
year = {2026},
author = {Luo, D and Lu, F and Yang, L and Gan, Z and Zhang, X and Zhao, Z and Dong, R},
title = {Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42420833},
issn = {1471-2164},
support = {GZSTYYCYJSTX-202605//Guizhou Modern Agricultural Industry Technology System of China/ ; 2024 (No. 079//the Guizhou Provincial Key Technology R&D Program/ ; 32460918//the National Natural Science Foundation of China/ ; },
mesh = {*Probiotics/pharmacology ; Multiomics ; *Phenols/toxicity ; Animals ; *Gastrointestinal Microbiome/drug effects ; Bacillus subtilis ; Lipid Metabolism/drug effects ; Metabolomics ; },
abstract = {BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed.

RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT‒qPCR and ELISA.

CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.},
}

*Probiotics/pharmacology
Multiomics
*Phenols/toxicity
Animals
*Gastrointestinal Microbiome/drug effects
Bacillus subtilis
Lipid Metabolism/drug effects
Metabolomics

@article {pmid42526667,
year = {2026},
author = {Cui, P and Zhang, H and Hu, T and Huang, Q and Hu, X and Wang, Q and Diwan, AD and Wang, T and Zhao, X and Lu, S and Chen, X},
title = {The Metabolite indole-3-acetic acid of Bacteroides ovatus ameliorates ovariectomy-induced bone loss by activating AhR and inhibiting oxidative stress.},
journal = {Free radical biology & medicine},
volume = {255},
number = {},
pages = {476-494},
doi = {10.1016/j.freeradbiomed.2026.07.050},
pmid = {42526667},
issn = {1873-4596},
mesh = {Animals ; Ovariectomy/adverse effects ; Female ; *Oxidative Stress/drug effects ; Mice ; *Bacteroides/metabolism ; Humans ; *Indoleacetic Acids/metabolism/pharmacology ; *Osteoporosis, Postmenopausal/metabolism/pathology/etiology/microbiology/prevention & control ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Gastrointestinal Microbiome ; *Bone Resorption/pathology/metabolism/prevention & control ; Osteoclasts/metabolism/drug effects ; *Basic Helix-Loop-Helix Proteins/metabolism/genetics ; Dysbiosis ; },
abstract = {Postmenopausal osteoporosis represents a systemic skeletal condition distinguished by diminished bone mass and heightened skeletal fragility. Emerging evidence has highlighted a significant relationship between bone metabolism and disturbances in gut microbiota (GM) homeostasis. However, the exact mechanisms by which GM dysbiosis contributes to postmenopausal osteoporosis remain insufficiently understood. Herein, integrating weighted gene co-expression network analysis with machine learning, a notable depletion of Bacteroides ovatus (B. ovatus) was identified in the GM of women with postmenopausal osteoporosis. Metagenomic sequencing further validated the reduced abundance of B. ovatus in ovariectomized (OVX) mice. Notably, live B. ovatus (LBO), but not heat-killed B. ovatus (KBO), effectively mitigated bone loss in OVX mice and restored intestinal mucosal barrier integrity. Both untargeted and targeted metabolomic profiling revealed substantial alterations in tryptophan metabolism in OVX mice, particularly a significant reduction in indole-3-acetic acid (IAA). Oral supplementation with IAA notably alleviated bone loss in OVX mice. Mechanistically, IAA stimulated AhR, enhancing NQO1 expression, reducing intracellular ROS buildup, and ultimately suppressing osteoclast differentiation and bone resorption. This investigation demonstrates, for the first time, the protective effects of B. ovatus and its metabolite IAA in counteracting estrogen deficiency-induced bone loss and may present a promising microbial-targeted strategy for osteoporosis prevention.},
}

Animals
Ovariectomy/adverse effects
Female
*Oxidative Stress/drug effects
Mice
*Bacteroides/metabolism
Humans
*Indoleacetic Acids/metabolism/pharmacology
*Osteoporosis, Postmenopausal/metabolism/pathology/etiology/microbiology/prevention & control
*Receptors, Aryl Hydrocarbon/metabolism/genetics
Gastrointestinal Microbiome
*Bone Resorption/pathology/metabolism/prevention & control
Osteoclasts/metabolism/drug effects
*Basic Helix-Loop-Helix Proteins/metabolism/genetics
Dysbiosis

@article {pmid42571814,
year = {2026},
author = {Ge, S and Sun, M and He, J and Pan, Y and Xu, Y and Wang, L and Luo, R and Zhong, Y and Wang, Y and Huang, J and Hu, M and Huang, Z and Wu, G and Wan, Y and Mo, L and Wu, F and Nie, C and Zhou, H and He, Y and Ma, Z and He, X and Gao, J},
title = {Gut microbial DL-endopeptidase protects against alcohol-associated liver disease via hepatocyte NOD2 signaling.},
journal = {Free radical biology & medicine},
volume = {255},
number = {},
pages = {712-729},
doi = {10.1016/j.freeradbiomed.2026.08.020},
pmid = {42571814},
issn = {1873-4596},
mesh = {Animals ; *Nod2 Signaling Adaptor Protein/metabolism/genetics ; Mice ; *Hepatocytes/metabolism/pathology/drug effects ; Signal Transduction ; *Liver Diseases, Alcoholic/pathology/microbiology/genetics/metabolism/prevention & control ; *Gastrointestinal Microbiome ; Humans ; Mice, Knockout ; Ethanol/toxicity ; Male ; Liver/pathology/metabolism/drug effects ; Mice, Inbred C57BL ; Oxidative Stress ; Acetylmuramyl-Alanyl-Isoglutamine/analogs & derivatives/pharmacology ; },
abstract = {Chronic alcohol consumption disrupts gut-liver homeostasis not only by inducing direct hepatotoxic injury, but also by perturbing host-microbial defense mechanisms that normally protect the liver from metabolic and inflammatory stress. We show that hepatocyte-specific deletion of Nod2 exacerbates ethanol-induced steatosis, oxidative stress, and mitochondrial dysfunction, establishing NOD2 as a critical protective factor in alcohol-associated liver disease (ALD). Importantly, beyond its direct hepatotoxic effects, ethanol exposure simultaneously diminishes this protective NOD2 pathway by limiting microbiota-derived ligand availability. Guided by this functional deficit, clinical metagenomic analysis (n = 1516) revealed that alcohol consumption is associated with a selective depletion of gut microbial DL-endopeptidase, a rate-limiting enzyme for NOD2 ligand generation, which inversely correlated with liver injury severity. Mice receiving fecal microbiota from donors with low DL-endopeptidase activity showed increased susceptibility to ALD. Importantly, supplementation with a NOD2 ligand or its clinical analogue, mifamurtide, restored mitochondrial homeostasis and alleviated liver injury. Together, these findings identify the gut microbial DL-endopeptidase-NOD2 axis as a key protective mechanism against ethanol-induced liver injury and a promising therapeutic target in alcohol-associated liver disease.},
}

Animals
*Nod2 Signaling Adaptor Protein/metabolism/genetics
Mice
*Hepatocytes/metabolism/pathology/drug effects
Signal Transduction
*Liver Diseases, Alcoholic/pathology/microbiology/genetics/metabolism/prevention & control
*Gastrointestinal Microbiome
Humans
Mice, Knockout
Ethanol/toxicity
Male
Liver/pathology/metabolism/drug effects
Mice, Inbred C57BL
Oxidative Stress
Acetylmuramyl-Alanyl-Isoglutamine/analogs & derivatives/pharmacology

@article {pmid42586263,
year = {2026},
author = {Zhou, Y and Guo, Q and Zhao, X and Zhang, W and Zhang, H and Huang, S and He, Z and Xie, Y and Zhang, W and Gu, J and Pan, S and Li, W},
title = {Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.},
journal = {Virologica Sinica},
volume = {41},
number = {4},
pages = {791-805},
doi = {10.1016/j.virs.2026.08.010},
pmid = {42586263},
issn = {1995-820X},
mesh = {Humans ; *Virome ; *Stomach Neoplasms/virology/blood ; *Anelloviridae/isolation & purification/genetics/classification ; Feces/virology ; Metagenomics ; Female ; Bacteriophages/genetics/isolation & purification/classification ; Male ; Middle Aged ; Aged ; Tumor Microenvironment ; },
abstract = {Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.},
}

Humans
*Virome
*Stomach Neoplasms/virology/blood
*Anelloviridae/isolation & purification/genetics/classification
Feces/virology
Metagenomics
Female
Bacteriophages/genetics/isolation & purification/classification
Male
Middle Aged
Aged
Tumor Microenvironment

@article {pmid42698579,
year = {2026},
author = {Murugesan, M and Thankappan, S and Mageshwaran, V and Ramasamy, R and Singaram, A},
title = {Decoding the functional diversity of plant growth-promoting bacterial communities in the soils of Western Ghats, Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1865342},
doi = {10.3389/fmicb.2026.1865342},
pmid = {42698579},
issn = {1664-302X},
abstract = {Western ghats in India, one of the world's biodiversity hot spots is the reservoirs of microbial resources having agricultural and industrial significance. However, the diversity of plant growth-promoting microbial communities associated with the plants and soil in the Western Ghats is untapped vault. The current emphasis on natural farming is more depending on the indigenous microbial communities and their metabolic functions towards sustainable one -health. With this background, the present study examines the bacterial diversity of soils from the Western Ghats of Nilgiris, Coimbatore and Dindigul regions. Among the 10 soil samples collected (S1 to S10), three soil samples (S2, S4 and S6) representing respective three regions were subjected for metagenomic studies based on their distinct soil chemical and biological properties. The computational analysis of the metagenome revealed the core genus Bradhyrhizobium in all soil samples, while Trebonia, Arthrobacter, Streptomyces, and Pseudomonas are the next most abundant genera, which varied substantially. The results collectively demonstrate that soil sample from Dindigul harbours the richest and most diverse microbial community among the three regions. In culturable studies, a total of 101 bacterial isolates were obtained from 10 soil samples (S1 to S10). Among them four Gram-negative bacterial isolates showed potential plant growth-promoting attributes, such as Ammonia, Indole Acetic Acid, Hydrogen cyanide and siderophore production, phosphorus, potassium, and zinc solubilization. The 16S rDNA analysis revealed that the bacterial isolates were Pseudomonas glycinae S6B1, Pseudomonas tolaasii S2B3, Pseudomonas azotoformans S9H10, and Pseudomonas poae S10B2. The isolate, S10B2, exhibited the maximum inhibition, with 81.25%, 70.1%, and 35% against plant pathogenic fungi, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, respectively, indicating strong biocontrol potential. The effect of bacterial inoculants on chick pea (Cicer arietinum var. JG 62), showed that P. glycinae S6B1 significantly promoted plant growth such as root length, shoot length, and fresh/dry biomass. These findings unlock the core microbiome of soils of Western Ghats, which can be utilized to develop a synthetic microbial consortium to boost agricultural productivity.},
}

@article {pmid41932647,
year = {2026},
author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L},
title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {53},
number = {9},
pages = {1688-1702},
doi = {10.1016/j.jgg.2026.03.023},
pmid = {41932647},
issn = {1673-8527},
mesh = {Female ; Animals ; *Probiotics/pharmacology/administration & dosage ; *Aging/drug effects/physiology ; *Ovary/drug effects/physiology ; Mice ; Gastrointestinal Microbiome/drug effects ; Fecal Microbiota Transplantation ; Humans ; },
abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.},
}

Female
Animals
*Probiotics/pharmacology/administration & dosage
*Aging/drug effects/physiology
*Ovary/drug effects/physiology
Mice
Gastrointestinal Microbiome/drug effects
Fecal Microbiota Transplantation
Humans

@article {pmid42097354,
year = {2026},
author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S},
title = {Integrative machine learning models to unravel gut microbial dysbiosis and functional disruption in polycystic ovary syndrome.},
journal = {F&S science},
volume = {7},
number = {5},
pages = {394-407},
doi = {10.1016/j.xfss.2026.04.005},
pmid = {42097354},
issn = {2666-335X},
mesh = {*Polycystic Ovary Syndrome/microbiology/metabolism ; Female ; Humans ; *Dysbiosis/microbiology ; *Machine Learning ; *Gastrointestinal Microbiome ; Case-Control Studies ; Metagenomics ; },
abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared with healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PCOS MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.

RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of proinflammatory taxa, such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals, including Roseburia hominis and Prevotella copri. These compositional shifts indicate a proinflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome-based machine learning models achieved a diagnostic accuracy of 84.25% (area under the curve 0.93), underscoring their predictive potential.

CONCLUSION: The gut microbiome in PCOS is characterized by a proinflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.},
}

*Polycystic Ovary Syndrome/microbiology/metabolism
Female
Humans
*Dysbiosis/microbiology
*Machine Learning
*Gastrointestinal Microbiome
Case-Control Studies
Metagenomics

@article {pmid42379395,
year = {2026},
author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, PP and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM},
title = {Oat-Rich Low-Gluten Diet Modulates Plasma Short-Chain Fatty Acids without Significant Changes in Fecal Microbiome or Inflammatory Markers-A Randomized Clinical Trial in People with Cardiometabolic Risk.},
journal = {The Journal of nutrition},
volume = {156},
number = {9},
pages = {101690},
doi = {10.1016/j.tjnut.2026.101690},
pmid = {42379395},
issn = {1541-6100},
mesh = {Humans ; *Avena ; *Feces/microbiology ; Male ; *Fatty Acids, Volatile/blood ; Female ; Biomarkers/blood ; Middle Aged ; Cardiometabolic Risk Factors ; *Diet ; *Inflammation/blood ; Oryza ; *Cardiovascular Diseases ; Adult ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.

OBJECTIVES: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers (IM) during a 6-wk oat- or rice-rich LGD in individuals with increased cardiometabolic risk.

METHODS: The participants (n = 69) were allocated into 2 parallel groups following a 6-wk LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (NovaSeq X Plus) and characterized using metagenomic phylogenetic analysis, version 4 (MetaPhlAn4). Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by ultra-HPLC-mass spectrometry, and IM were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with a linear mixed-effects model.

RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. In particular, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (PtimeXgroup = 0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (PTimeXgroup = 0.025) and more changes in the microbiome. This is possibly due to more substantial dietary changes from low rice consumption compared with the habitual diet at baseline. No significant differences between or changes within the groups in IM were observed.

CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and IM in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome toward a potentially unfavorable direction. This trial was registered at clinicaltrials.gov as NCT05526092.},
}

Humans
*Avena
*Feces/microbiology
Male
*Fatty Acids, Volatile/blood
Female
Biomarkers/blood
Middle Aged
Cardiometabolic Risk Factors
*Diet
*Inflammation/blood
Oryza
*Cardiovascular Diseases
Adult
*Microbiota
*Gastrointestinal Microbiome

@article {pmid42392574,
year = {2026},
author = {Vita, AA and Brown, J and Norby-Adams, L and Ghanem, N and Weir, TL and Goldenberg, JZ},
title = {Microbial-Derived Polyphenol Metabolites and the Gut Microbiota: A Scoping Review of Clinical Studies.},
journal = {The Journal of nutrition},
volume = {156},
number = {9},
pages = {101700},
doi = {10.1016/j.tjnut.2026.101700},
pmid = {42392574},
issn = {1541-6100},
mesh = {Humans ; *Polyphenols/metabolism ; *Gastrointestinal Microbiome/physiology ; Bacteria/metabolism ; },
abstract = {BACKGROUND: Dietary (poly)phenols are widely recognized for their health-promoting properties, yet their bioactivity is largely contingent upon gut microbial metabolism. Individual differences in microbiome composition lead to variable production of microbial-derived (poly)phenol metabolites (MPMs) and thus contribute to divergent health outcomes.

OBJECTIVES: This scoping review aimed to systematically map the scope of clinical evidence reporting relationships between MPMs and gut microbiota composition and function, highlighting research gaps to guide future investigations.

METHODS: Using predefined search criteria, 2 reviewers identified human clinical studies reporting relationships between metabolite concentrations and microbiome outcomes.

RESULTS: Fifty-six studies were included. Evidence was frequently focused on phenolic acids (n = 20), phytoestrogens (n = 18), and urolithins (n = 17), with relationships between microbiota and other MPMs being reported in only 1 to 2 studies. The majority of studies across MPM categories used 16S rRNA gene sequencing for the identification of gut microbiota (n = 42), among other methods, with only 6 studies using metagenomic shotgun sequencing, thus limiting taxonomic resolution and functional inference. Findings revealed recurrent associations between specific microbes and MPMs. Although some reflected known producer taxa (e.g., Gordonibacter and urolithins), others may represent broader community-level interactions (e.g., Alistipes and equol). However, these results varied across (poly)phenol class, intervention type, and host-specific context.

CONCLUSIONS: This scoping review identified recurrent microbiota-MPM associations alongside major evidence gaps, including limited functional microbiome characterization and sparse investigation of several MPM classes/subclasses (e.g., resveratrol-, flavanone-, and flavan-3-ol-related MPMs). Future research using standardized, high-resolution multi-omics approaches is needed to improve the identification of reproducible microbial signatures and mechanisms underlying (poly)phenol metabolism and to link these features with functional health outcomes.},
}

Humans
*Polyphenols/metabolism
*Gastrointestinal Microbiome/physiology
Bacteria/metabolism

@article {pmid42693766,
year = {2026},
author = {Baños, E and Segura, CR and De Boer, EJ and Cundy, AB and Barrera, XT and Nogué, S and Holman, LE and Rius, M},
title = {Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70200},
doi = {10.1111/1755-0998.70200},
pmid = {42693766},
issn = {1755-0998},
support = {TED2021-132228B-C21//TEMPOINVASIONS/ ; TED2021-132228B-C22//TEMPOINVASIONS/ ; PID2023-146307OB//TEMPOINVASIONS/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Biota ; },
abstract = {Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.},
}

*DNA Barcoding, Taxonomic/methods
*Geologic Sediments/microbiology
*Metagenomics/methods
RNA, Ribosomal, 18S/genetics
Electron Transport Complex IV/genetics
*Biota

@article {pmid42694408,
year = {2026},
author = {Young, D and Stüer-Patowsky, K and Huang, L and Elshahed, MS and Youssef, NH and Hanafy, R and Cheng, Y and Moon, CD and Soni, P and Joshi, A and Stabel, M and Ochsenreither, K and Dagar, SS and Hillman, E and Solomon, KV and Fliegerová, KO and Griffith, GW and Callaghan, TM and Podmirseg, SM and Sczyrba, A and Flad, V and Lebuhn, M and Wurzbacher, C},
title = {Full ribosomal operon sequencing of anaerobic gut fungi (phylum Neocallimastigomycota): insights on its markers and phylogenetic resolution.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e195921},
pmid = {42694408},
issn = {2210-6340},
abstract = {The phylogenetic affiliations of anaerobic gut fungi (Neocallimastigomycota) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.},
}

@article {pmid42694564,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Sun, Y},
title = {Synergistic Regulation of Alzheimer's Disease and Intestinal Microbiota Metabolism Mediated by the Gut-Brain Axis: A Comprehensive Analysis from a Multidisciplinary Perspective.},
journal = {International journal of medical sciences},
volume = {23},
number = {9},
pages = {2939-2962},
pmid = {42694564},
issn = {1449-1907},
mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/immunology/therapy ; *Gastrointestinal Microbiome/immunology/physiology ; *Brain/metabolism/immunology ; Animals ; Multiomics ; *Brain-Gut Axis/immunology/physiology ; *Dysbiosis/microbiology/immunology ; },
abstract = {Alzheimer's disease (AD), as a neurodegenerative disease with the interaction of multiple factors, has a close association between its pathological process and the metabolic imbalance of the gut microbiota mediated by the gut-brain axis. This review systematically summarizes the molecular mechanisms by which the gut microbiota regulates the functions of the central nervous system bidirectionally through molecular pathways such as metabolites (e.g., short-chain fatty acids, tryptophan-kynurenine metabolites), immunomodulatory mediators (e.g., cytokines, chemokines), and bioactive substances (e.g., γ-aminobutyric acid, 5-hydroxytryptophan) via the gut-brain axis. It synthesizes current evidence suggesting the imbalance of microbiota homeostasis may be closely associated with the core pathologies of AD (including β-amyloid deposition and tau protein hyperphosphorylation) through mechanisms such as the activation of the C/EBPβ-AEP signaling pathway, induction of chronic neuroinflammation, oxidative stress cascade reactions, and metabolic network remodeling. These findings, primarily derived from preclinical models and correlational human studies, indicate potential mechanisms but require further causal validation and rigorous clinical translation, including the downregulation of butyrate synthesis pathways and their associated epigenetic and immunomodulatory consequences (as mechanistically dissected in Section 5.2). Multi-omics integration (metagenomics, metabolomics, spatial transcriptomics) has delineated characteristic microbial and metabolic alterations in AD, while computational approaches are beginning to elucidate the complex networks underlying these associations (see Sections 6 and 7 for details).Intervention strategies based on microbiota regulation (such as microbiota-targeted dietary interventions and postbiotics) are emerging as promising approaches, although their clinical applications remain in early stages. Preliminary evidence suggests that fecal microbiota transplantation may improve cognitive outcomes in AD patients with comorbid conditions; however, rigorous randomized controlled trials are essential to validate its efficacy and safety. Critically, translating these mechanistic insights into clinical practice requires overcoming three translational bottlenecks: inferring causality from correlational multi-omics data, resolving species/strain-level functional heterogeneity masked by genus-level taxonomy, and establishing standardized safety protocols for live biotherapeutic products. Addressing these challenges defines the near-term roadmap for precision medicine in AD. However, current research still faces challenges such as the heterogeneity of cross-omics data, the lack of technical standardization, and insufficient interdisciplinary cooperation mechanisms. In the future, it is necessary to promote the early molecular diagnosis and personalized targeted treatment of AD through longitudinal multi-omics dynamic monitoring, modeling of the microbiota-host interaction network, and optimization of the ethical-translational medicine framework.},
}

Humans
*Alzheimer Disease/microbiology/metabolism/immunology/therapy
*Gastrointestinal Microbiome/immunology/physiology
*Brain/metabolism/immunology
Animals
Multiomics
*Brain-Gut Axis/immunology/physiology
*Dysbiosis/microbiology/immunology

@article {pmid42694612,
year = {2026},
author = {Davis, EE and Younger, J and Burridge, C and Armbrecht, L},
title = {How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag113},
pmid = {42694612},
issn = {2635-0041},
abstract = {MOTIVATION: Sedimentary ancient DNA (sedaDNA) is genetic material extracted from paleoarchives. It provides insights into the composition and dynamics of ecosystems over time. Such information can be crucial in anticipating how ecological communities may respond to environmental shifts within the context of the current climate crisis. However, challenges exist in accurately verifying ancient DNA from ecologically significant vertebrate species (e.g. fishes, aquatic birds, and mammals). These species occur only in trace amounts in sedimentary records. Here, we benchmark a stringent bioinformatic pipeline using synthetic and empirical metagenomic sedaDNA data from IODP Expedition 382 (Scotia Sea). Our objectives are threefold: (i) test taxonomic assignment precision for rare marine eukaryotes, (ii) evaluate taxonomic assignment sensitivity across different sediment ages, and (iii) establish the minimum sequence quantity necessary for robust identification.

RESULTS: We demonstrate that taxonomic assignment precision varied significantly with sequence quantity and metagenomic context. Assignment sensitivity decreased with taxonomic rank and database representation. Reliable detection of low-abundance taxa in sedaDNA is achievable with 250 and 500 DNA fragments at the family and genus level, respectively. The reanalysis of IODP Exp. 382 sedaDNA data, using a custom built marine vertebrate-focused reference database, resulted in the first genetic reconstruction of the vertebrate community in the Scotia Sea. This lays the groundwork for future investigations into the presence and biodiversity of Southern Ocean vertebrates using sedaDNA.

All project related scripts and generated simulated datasets are available in ae_fishing_benchmark repository (https://github.com/33davis/ae_fishing_benchmark). The demultiplexed raw data in relation to the IODP Exp. 382 U1538 reanalysed during this study is available in the NCBI Sequence Read Archive database (https://www.ncbi.nlm.nih.gov/sra) under Accession code/BioProject PRJNA861836 (BioSamples SAMN29928044 - SAMN29928123) and includes metadata for each sediment and control sample.},
}

@article {pmid42695179,
year = {2026},
author = {Nett, N and Dumack, K},
title = {A Pan-European Whole-Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70112},
doi = {10.1111/jeu.70112},
pmid = {42695179},
issn = {1550-7408},
support = {556896378//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; },
mesh = {*Wastewater/microbiology/parasitology ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Europe ; *Microbiota ; *Eukaryota/classification/genetics/isolation & purification ; Seasons ; Animals ; },
abstract = {Microbial communities entering wastewater treatment plants (WWTPs) through untreated sewage represent an important interface between human, environmental, and treatment-associated microbiomes, yet our understanding of their biogeography remains poorly resolved, particularly for microbial eukaryotes. Using shotgun metagenomic time-series data from influent samples of seven WWTPs across a European latitudinal gradient, we analyzed the taxonomic composition and dynamics of bacteria, protists, fungi, and microscopic metazoa. Influent community composition varied with geographic location and season, with a pronounced north-south divergence driven by dominant taxa and stronger seasonal shifts observed at higher latitudes. Cross-domain associations were pervasive, suggesting that co-varying bacterial and eukaryotic components structure the incoming microbial pool. Our findings provide a pan-European baseline for whole-microbiome wastewater surveillance and highlight that influent communities differ regionally and seasonally. These patterns may be relevant for downstream treatment-stage microbiomes, but direct effects on reactor community assembly and treatment performance require targeted sampling across treatment stages.},
}

*Wastewater/microbiology/parasitology
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Europe
*Microbiota
*Eukaryota/classification/genetics/isolation & purification
Seasons
Animals

@article {pmid42697668,
year = {2026},
author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T},
title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107299},
doi = {10.1016/j.pestbp.2026.107299},
pmid = {42697668},
issn = {1095-9939},
mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; },
abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.},
}

*Rhizosphere
Fungi/drug effects/genetics
Oryza/microbiology
Bacteria/drug effects/genetics
Metagenomics
*Fungicides, Industrial/pharmacology
Soil Microbiology
*Microbiota/drug effects
Metagenome

@article {pmid42687165,
year = {2026},
author = {Wang, Y and Wang, L and Cai, Z and Yu, L and Guo, Y and Zhang, L and Zhu, M and Liu, Z and Zhao, Y and Liu, L and Cao, A},
title = {Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42687165},
issn = {1471-244X},
mesh = {Humans ; *Diet, Ketogenic ; *Fecal Microbiota Transplantation ; Female ; Male ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/therapy/microbiology/diet therapy ; Child ; Child, Preschool ; Treatment Outcome ; },
abstract = {OBJECTIVE: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, along with restricted, repetitive patterns of behavior. It is often accompanied by gastrointestinal dysfunction and gut microbiota dysbiosis. Fecal Microbiota Transplantation (FMT) and the Ketogenic Diet (KD) are interventions targeting the gut microbiota for ASD.

METHODS: 30 participants were diagnosed with ASD according to DSM-5 and ADOS-2. ASD core symptoms were evaluated with CARS and ABC. Gut microbiota composition was analyzed by shotgun metagenomic sequencing.

RESULTS: Both groups demonstrated significant improvements in core symptoms. In the FMT group, the mean CARS score significantly decreased from 34.87 to 33.53 (p < 0.01); in the KD group, it declined from 35.13 to 33 (p < 0.01). The mean ABC score reduced from 79.93 to 69.33 (p = 0.064) in the FMT group and from 63.07 to 42.73 (p < 0.01) in the KD group. Following the intervention, no statistically significant changes were observed in α-diversity or β-diversity within either group. LEfSe analysis revealed distinct post-intervention microbial signatures: FMT significantly enriched butyrate-producing taxa (Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus), while KD elevated Blautia massiliensis and decreased propionate metabolism -associated taxa (Veillonella sp. S12025-13 and Veillonella nakazawae). KEGG enrichment analysis revealed that KD enriched propionate metabolism (Fold enrichment = 3.747, q = 0.010) and aromatic compound degradation (Fold enrichment = 3.591, q = 0.010).

CONCLUSIONS: Both interventions significantly improved clinical symptoms among children with ASD, potentially through distinct patterns of gut microbiota modulation.

CLINICAL TRIALS NUMBER: NCT06348433 (03/21/2024).},
}

Humans
*Diet, Ketogenic
*Fecal Microbiota Transplantation
Female
Male
*Gastrointestinal Microbiome
*Autism Spectrum Disorder/therapy/microbiology/diet therapy
Child
Child, Preschool
Treatment Outcome

@article {pmid42687643,
year = {2026},
author = {Jeon, D and Unno, T},
title = {Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {8},
pages = {e2605007},
doi = {10.71150/jm.2605007},
pmid = {42687643},
issn = {1976-3794},
support = {RS-2025-02633155//Rural Development Administration/ ; },
mesh = {Animals ; *Metagenomics/methods ; Cattle ; *Plasmids/genetics ; Swine ; Humans ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Drug Resistance, Multiple, Bacterial/genetics ; Metagenome ; },
abstract = {While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.},
}

Animals
*Metagenomics/methods
Cattle
*Plasmids/genetics
Swine
Humans
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
*Drug Resistance, Multiple, Bacterial/genetics
Metagenome

@article {pmid42687714,
year = {2026},
author = {Velsko, IM and Hübner, A and Fagernäs, Z and Yates, JAF and Mann, AE and Hofman, CA and Ozga, AT and Lewis, CM and Speller, C and Fiddyment, S and Francken, M and Wahl, J and Krause, J and Radini, A and King, T and Warinner, C},
title = {The Oral Microbiome of King Richard III of England.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70350},
pmid = {42687714},
issn = {2692-7691},
support = {//Werner Siemens Stiftung/ ; //Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy/ ; //Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM)/ ; //Max Planck Society/ ; },
mesh = {Humans ; *Microbiota/genetics ; England ; *Dental Calculus/microbiology/history ; DNA, Ancient/analysis ; History, 15th Century ; *Mouth/microbiology ; History, Medieval ; History, Ancient ; Phylogeny ; Metagenome/genetics ; },
abstract = {OBJECTIVES: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452-1485).

MATERIALS AND METHODS: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome-assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity.

RESULTS: The dental calculus of King Richard III was well-preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated.

DISCUSSION: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000 years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well-preserved.},
}

Humans
*Microbiota/genetics
England
*Dental Calculus/microbiology/history
DNA, Ancient/analysis
History, 15th Century
*Mouth/microbiology
History, Medieval
History, Ancient
Phylogeny
Metagenome/genetics

@article {pmid42688151,
year = {2026},
author = {Cai, S and Xu, X and Sun, X and Luo, Q and Chen, W and Wang, X and Zhu, J and Liu, Y and Xiao, L and Zhang, H and Zou, Y and Zhong, Y},
title = {Alleviation of allergic rhinitis symptoms in an animal model by Lactiplantibacillus plantarum BGI-N6.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1923543},
pmid = {42688151},
issn = {1664-3224},
mesh = {Animals ; *Probiotics/therapeutic use ; Disease Models, Animal ; *Rhinitis, Allergic/immunology/therapy/microbiology ; Rats ; *Lactiplantibacillus plantarum/immunology ; Cytokines/blood ; *Gastrointestinal Microbiome/immunology ; Nasal Mucosa/immunology/pathology ; Male ; },
abstract = {Allergic rhinitis (AR) is a chronic inflammatory disease with rising global prevalence and a substantial public health burden. Current treatments have limited efficacy and tolerability, highlighting the need for new strategies. Probiotics represent a promising approach due to their ability to modulate gut microbiota and host immunity. Here, we investigated the preventive potential of Lactiplantibacillus plantarum BGI-N6 in an OVA/ALUM-induced AR rat model. BGI-N6 administration alleviated AR symptoms and nasal mucosal pathology, reduced key allergic mediators, shifted serum immunoglobulin and cytokine levels toward normal, and restored the Th1/Th2/Th17/Treg balance. Metagenomic sequencing of cecal contents showed that these effects were accompanied by expansion of Bacteroidota-affiliated SCFA-producing taxa, restoration of microbial functional capacity, and identification of 41 core functional genes (KEGG Orthologues) consistently shifted across all three dose groups, with Bacteroides showing the strongest enrichment. Correlation analyses further connected these microbial shifts with immune parameters. These findings support BGI-N6 as a probiotic intervention for AR and implicate gut microbiota remodeling as a central correlate of probiotic-induced immunomodulation.},
}

Animals
*Probiotics/therapeutic use
Disease Models, Animal
*Rhinitis, Allergic/immunology/therapy/microbiology
Rats
*Lactiplantibacillus plantarum/immunology
Cytokines/blood
*Gastrointestinal Microbiome/immunology
Nasal Mucosa/immunology/pathology
Male

@article {pmid42688840,
year = {2026},
author = {Li, J and Liu, Y and Gao, T and Ding, H and Hu, R and Wang, Y and Wu, B},
title = {Progress in interventions for vaginal microecology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1888581},
pmid = {42688840},
issn = {2235-2988},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota ; *Probiotics/administration & dosage/therapeutic use ; *Dysbiosis/therapy/microbiology ; Prebiotics/administration & dosage ; Synbiotics/administration & dosage ; },
abstract = {A balanced vaginal microbiome is fundamental to reproductive and gynecologic health, yet dysbiosis is common and clinically consequential. This narrative review synthesizes recent advances in microecological interventions, including probiotic, prebiotic, and synbiotic regimens; combination therapies; and vaginal microbiota transplantation. We place a particular focus on emerging delivery platforms like hydrogel-based carriers, which improve probiotic viability, mucosal adhesion, and controlled release. The review also explores how metagenomic analysis is refining community state typing, identifying pathogenic consortia, and enabling data-driven patient stratification and response monitoring. Despite these advances, key challenges remain, such as strain selection, functional validation, colonization durability, heterogeneous clinical endpoints, and clear regulatory pathways for live biotherapeutics. Future priorities must include developing functionally defined strain consortia, standardizing clinical outcomes, integrating multi-omics with biomaterials engineering, and conducting rigorous multicenter trials to deliver durable, safe, and truly individualized therapies.},
}

Humans
*Vagina/microbiology
Female
*Microbiota
*Probiotics/administration & dosage/therapeutic use
*Dysbiosis/therapy/microbiology
Prebiotics/administration & dosage
Synbiotics/administration & dosage

@article {pmid42690486,
year = {2026},
author = {Wen, Y and Luo, Z and Li, Z and Li, K and Li, J and Yin, S and Zou, Y and Zhang, H and Zhang, Y and Chen, K and Zhang, Y and Liu, S and Chen, Z and Yu, L and Ding, Y},
title = {Oral and gut microbiota profiles in patients with locally advanced rectal cancer with varying responses to neoadjuvant chemoradiotherapy.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42690486},
issn = {1438-7948},
support = {2023A0060//Science and Technology Plan Project of Jiangxi Provincial Administration of Traditional Chinese Medicine/ ; 2024A1515013292//Guangdong Basic and Applied Basic Research Fundation/ ; 2025A1515010567//Guangdong Basic and Applied Basic Research Fundation/ ; 2026A1515012094//Guangdong Basic and Applied Basic Research Fundation/ ; 32300085//National Natural Science Foundation of China/ ; 82504340//National Natural Science Foundation of China/ ; 82473567//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy/pathology ; *Neoadjuvant Therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Chemoradiotherapy ; Aged ; Feces/microbiology ; Saliva/microbiology ; },
abstract = {Recent research has focused on gut bacteria in colorectal cancer, but the influence of other microbiota, including oral and nonbacterial gut microbiota, on treatment efficacy remains insufficiently explored. This study aimed to investigate their relationship with the efficacy of neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC). Saliva and fecal samples were collected from patients with LARC before treatment. Shotgun metagenomic sequencing was used to profile bacterial, archaeal, eukaryotic, and viral taxonomic groups and to examine oral and gut microbial functions. An artificial intelligence-based prediction model was developed by integrating oral and gut microbiome data with clinical information. Statistical analyses compared diversity and response-associated microbial features between responders and non-responders to nCRT. Response-associated differences were observed in bacterial and nonbacterial taxonomic profiles and in oral and gut microbial functional profiles. In the internal test subset, the integrated analysis yielded an observed AUC of 0.917. Given the small cohort and the exploratory comparison of candidate classifiers, this estimate requires confirmation in larger, independent cohorts. Baseline oral and gut microbiome profiles were associated with response to nCRT. Integrating microbiome and clinical features showed potential for response prediction, but the model remains exploratory and requires validation in larger, independent cohorts before clinical application. Retrospectively registered on 01/08/2026, NCT07346729.},
}

Humans
*Rectal Neoplasms/microbiology/therapy/pathology
*Neoadjuvant Therapy
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Chemoradiotherapy
Aged
Feces/microbiology
Saliva/microbiology

@article {pmid42692606,
year = {2026},
author = {Ma, C and Geng, R and Hou, Q and Zhao, Y and Yue, Y and Xue, T and Wen, L and Li, T and Yang, J and Hu, J},
title = {Structure and protection of Cichorium glandulosum polysaccharides against sarcopenic obesity through activating mitophagy via butyrate-GPR43-AMPK pathway.},
journal = {Carbohydrate polymers},
volume = {390},
number = {},
pages = {125722},
doi = {10.1016/j.carbpol.2026.125722},
pmid = {42692606},
issn = {1879-1344},
mesh = {Animals ; *Mitophagy/drug effects ; *Butyrates/metabolism ; AMP-Activated Protein Kinases/metabolism ; *Obesity/drug therapy/metabolism ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/drug effects ; *Asteraceae/chemistry ; *Polysaccharides/chemistry/pharmacology ; Male ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; },
abstract = {Sarcopenic obesity (SO) is a major complication of type 2 diabetes with limited therapeutic options. This study characterized CGP-A, a novel branched fructan (6.722 kDa) from Cichorium glandulosum. Its backbone consists of →1)-β-D-Fruf-(2→ and →6)-α-D-Glcp-(1→ residues, interspersed with →1,6)-β-D-Fruf-(2→ branching points. The side chains consist of terminal β-D-Fruf-(2→ units attached to the C-6 position of the fructofuranosyl residues in the backbone. In db/db mice, CGP-A dose-dependently ameliorated insulin resistance, hepatic steatosis, muscle loss and intestinal barrier dysfunction. Importantly, CGP-A significantly improved grip strength, reflecting an enhancement in muscle quality. Integrated multi-omics analysis combining metagenomics, multi-organ proteomics, and metabolomics revealed that CGP-A altered the gut microbiota, specifically enriching Ligilactobacillus, Bacteroides and Alistipes, while elevating serum butyrate. These findings suggest that butyrate may activate the GPR43-AMPK signaling pathway in both liver and skeletal muscle. Hepatic AMPK activation upregulated PPARα to enhance fatty acid oxidation; concurrently, muscular AMPK stimulated PINK1/Parkin-mediated mitophagy, restoring mitochondrial function and attenuating protein degradation. Antibiotic depletion abolished these effects, establishing the microbiota as a crucial mediator. These findings elucidate the gut microbiota-butyrate-GPR43-AMPK pathway through which CGP-A contributes to multi-organ metabolic improvements, offering a promising prebiotic strategy for managing SO.},
}

Animals
*Mitophagy/drug effects
*Butyrates/metabolism
AMP-Activated Protein Kinases/metabolism
*Obesity/drug therapy/metabolism
Mice
Receptors, G-Protein-Coupled/metabolism
Signal Transduction/drug effects
*Asteraceae/chemistry
*Polysaccharides/chemistry/pharmacology
Male
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL

@article {pmid42692700,
year = {2026},
author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z},
title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120303},
doi = {10.1016/j.foodres.2026.120303},
pmid = {42692700},
issn = {1873-7145},
mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; },
abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.},
}

Animals
*Metabolome
*Food Storage/methods
*Refrigeration
*Microbiota
*Geese/microbiology
Thiobarbituric Acid Reactive Substances/analysis
*Food Microbiology
Metabolomics
RNA, Ribosomal, 16S/genetics
Colony Count, Microbial
Bacteria
Chromatography, High Pressure Liquid

@article {pmid42692847,
year = {2026},
author = {Budinská, E},
title = {Microbiome in early cancer detection - biomarker potential and limitations.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {63-66},
doi = {10.48095/ccko2026S63},
pmid = {42692847},
issn = {1802-5307},
mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; },
abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.

AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.},
}

Humans
*Early Detection of Cancer/methods
*Neoplasms/diagnosis/microbiology
*Microbiota
*Biomarkers, Tumor

@article {pmid42693026,
year = {2026},
author = {Han, R and Gu, YW and Dong, J and Zhang, XZ and Cao, L and Wang, ZZ and Xiao, W and Jiang, S},
title = {[Mechanism of Tianshu Capsules in treating migraine rats based on gut microbiota].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {16},
pages = {4734-4743},
doi = {10.19540/j.cnki.cjcmm.20260509.701},
pmid = {42693026},
issn = {1001-5302},
mesh = {Animals ; *Migraine Disorders/drug therapy/metabolism/genetics/microbiology ; Rats, Sprague-Dawley ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration & dosage ; Calcitonin Gene-Related Peptide/genetics/metabolism ; Male ; Humans ; Disease Models, Animal ; Endothelin-1/metabolism/genetics/blood ; Capsules/administration & dosage ; Serotonin/blood/metabolism ; Proto-Oncogene Proteins c-fos/metabolism/genetics ; },
abstract = {This study aims to investigate the therapeutic effect of Tianshu Capsules(TS) on migraine rat model and explore its potential mechanism of action from the perspectives of the structure of the gut microbiota and functional pathway regulation. A migraine rat model was established via subcutaneous injection of nitroglycerin. The Sprague-Dawley rats were randomly divided into a control group, a model group, a low-dose TS group, a medium-dose TS group, a high-dose TS group, and an ibuprofen group. The efficacy of TS in improving migraine was evaluated by general condition observation and measurement of the craniofacial pain threshold. The expression of the gene c-fos in the trigeminal ganglion was determined by quantitative real-time polymerase chain reaction(PCR). The contents of endothelin-1(ET-1), calcitonin gene-related peptide(CGRP), and 5-hydroxytryptamine(5-HT) in serum were measured by enzyme-linked immunosorbent assay(ELISA). Fecal samples were subjected to metagenomic sequencing for systematic analysis of gut microbial diversity, taxonomic composition difference, and functional pathway changes of Kyoto Encyclopedia of Genes and Genomes(KEGG), and their correlations with behavioral and biochemical indices were further evaluated. The results show that TS significantly improves the increased body temperature and decreased craniofacial pain threshold in migraine rats. It also markedly suppresses the elevated expression levels of the gene c-fos in the trigeminal ganglion and reduces the levels of ET-1, CGRP, and 5-HT in serum. Metagenomic beta diversity analysis and differential taxonomic abundance analysis reveal that the migraine model induces significant gut microbiota dysbiosis, characterized by enrichment of harmful genera, including Streptococcus and Enterococcus, as well as a decline in the abundance of beneficial bacteria such as Allobaculum, Eubacterium, and Muribaculum. Functional pathway analysis results of KEGG further reveal that the relative abundances of pathways associated with biosynthesis of phenylalanine, tyrosine, and tryptophan, bacterial secretion system, citrate cycle, and biosynthesis of secondary metabolites are significantly decreased in the model group. TS intervention increased the abundance of the genus, such as Parabacteroides, Eubacterium, Allobaculum, and Muribaculum, while decreasing levels of microbiota, including Staphylococcus. TS also significantly upregulated pathways associated with barrier function(tight junction), amino acid biosynthesis pathways, and biosynthesis pathways of neurotransmitter precursors such as cysteine and methionine metabolism. In addition, it downregulated inflammatory pathways(Toll and IMD signaling) and pathways related to Staphylococcus aureus infection, thereby restoring the structure and function of the microbiota to a state close to those of the normal group. Spearman correlation analysis reveals that partial gut microbiota are significantly associated with migraine-related behavioral and biochemical indices(c-fos, ET-1, CGRP, and 5-HT). In conclusion, TS can regulate the disrupted gut microbiota structure and microbial functions related to neurotransmitter metabolism, intestinal barrier function, and inflammatory regulation in migraine model rats, which may be one of the potential key ways through which TS exert its anti-migraine effect.},
}

Animals
*Migraine Disorders/drug therapy/metabolism/genetics/microbiology
Rats, Sprague-Dawley
Rats
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/administration & dosage
Calcitonin Gene-Related Peptide/genetics/metabolism
Male
Humans
Disease Models, Animal
Endothelin-1/metabolism/genetics/blood
Capsules/administration & dosage
Serotonin/blood/metabolism
Proto-Oncogene Proteins c-fos/metabolism/genetics

@article {pmid42483952,
year = {2026},
author = {Oyama, LB},
title = {From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.},
journal = {Essays in biochemistry},
volume = {70},
number = {3},
pages = {387-398},
doi = {10.1042/EBC20250036},
pmid = {42483952},
issn = {1744-1358},
support = {BB/X012794/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; BB/Z515346/1//UK Research and Innovation (UKRI)/ ; },
mesh = {*Microbiota ; *Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics/therapeutic use ; Humans ; Animals ; },
abstract = {Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.},
}

*Microbiota
*Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics/therapeutic use
Humans
Animals

@article {pmid42484341,
year = {2026},
author = {Sato, Y and Uda, Y and Nagao, Y},
title = {Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0167726},
pmid = {42484341},
issn = {2165-0497},
support = {25K18347//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Rumen/microbiology/virology ; Cattle ; *Virome ; Female ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Microbiota ; Age Factors ; Ruminococcus/genetics ; },
abstract = {Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.},
}

Animals
*Rumen/microbiology/virology
Cattle
*Virome
Female
Metagenome
Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
*Microbiota
Age Factors
Ruminococcus/genetics

@article {pmid42488935,
year = {2026},
author = {Whelan, FJ},
title = {How the social lives of bacteria affect their pangenome.},
journal = {Essays in biochemistry},
volume = {70},
number = {3},
pages = {473-482},
doi = {10.1042/EBC20250039},
pmid = {42488935},
issn = {1744-1358},
support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; },
mesh = {*Bacteria/genetics ; *Genome, Bacterial ; *Microbiota/genetics ; Genetic Variation ; Phylogeny ; Metagenomics ; Computational Biology ; },
abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.},
}

*Bacteria/genetics
*Genome, Bacterial
*Microbiota/genetics
Genetic Variation
Phylogeny
Metagenomics
Computational Biology

@article {pmid42489451,
year = {2026},
author = {Roques, S and Tournayre, J and Dou, PS and Yanibada, B and Boudra, H and Popova, M and Morgavi, DP},
title = {Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0026926},
pmid = {42489451},
issn = {2165-0497},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Female ; Propanols/pharmacology ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; *Microbiota/drug effects ; Metagenomics ; Metabolome ; },
abstract = {Enteric methane emission from dairy cattle is an environmental challenge. The most efficient mitigation strategies nowadays include the use of methanogenesis inhibitors that specifically target the rumen methanogens. Specific inhibitors, such as 3-nitrooxypropanol (3-NOP), reduce methane emissions without negative effects on the products of fermentation that serve as energy metabolites for the host. However, the concomitant effects of methanogenesis inhibition on rumen microbiota and host metabolism are poorly characterized. Thus, the objective of this study was to explore the association between rumen microbiota and host metabolism when methanogenesis is inhibited. Thirteen dairy cows were used as controls, and 12 were supplemented with 3-NOP for 6 weeks. Rumen microbiota composition and activity were characterized using metagenomics and metatranscriptomics. The host metabolism was assessed in a previous publication by a metabolomic analysis of the plasma. Microbiota data were used as explanatory variables of the metabolome data in a multiblock sparse partial least squares analysis. Overall, the association between rumen microbiota and host metabolism was moderate. Notwithstanding this, a few downregulated transcripts related to glycolysis, hydrogen transfer, and protein synthesis, together with a decrease in the proportion of taxa of the Oscillospirales order, showed a correlation with host one-carbon metabolites (|r| > 0.6). These associations raised novel hypotheses that remain to be elucidated, especially with regard to the effects of dihydrogen on the accumulation of microbial glycolysis and methanogenesis metabolite intermediates.IMPORTANCEDairy cattle produce a substantial amount of methane, a potent greenhouse gas. Several strategies have been designed to reduce methane production by targeting the rumen microbiota. One such strategy specifically inhibits methanogens with a molecule called 3-nitrooxypropanol. This study uses an integrative data analysis approach, combining rumen microbiota and host metabolome information, to explore the consequences of inhibiting methanogenesis on the holobiont. This provides additional holistic insight into the effect of methane mitigation strategies on dairy cattle.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
Female
Propanols/pharmacology
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
*Gastrointestinal Microbiome/drug effects
Fermentation
*Microbiota/drug effects
Metagenomics
Metabolome

@article {pmid42496113,
year = {2026},
author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC},
title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0076326},
pmid = {42496113},
issn = {2165-0497},
support = {//Cornell University Start-up Funds/ ; CUP E53C25000400001//Ministry of University and Research/ ; 101045015//European Union/ ; NextGenerationEU//European Union/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Starch/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Metagenomics ; Dietary Supplements/analysis ; *Resistant Starch/metabolism ; },
abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.},
}

Humans
*Gastrointestinal Microbiome
*Starch/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Metagenomics
Dietary Supplements/analysis
*Resistant Starch/metabolism

@article {pmid42515960,
year = {2026},
author = {Kopp, AR and Uhlemann, AC},
title = {Gut dysbiosis and multidrug-resistant colonization in solid organ transplantation.},
journal = {Current opinion in organ transplantation},
volume = {31},
number = {5},
pages = {247-254},
doi = {10.1097/MOT.0000000000001303},
pmid = {42515960},
issn = {1531-7013},
mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Organ Transplantation/adverse effects/mortality ; Risk Factors ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Multiple, Bacterial ; Treatment Outcome ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Host-Pathogen Interactions ; *Bacteria/drug effects/pathogenicity ; Animals ; *Bacterial Infections/microbiology/drug therapy/immunology ; },
abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize recent advances in the understanding of the interplay between gut dysbiosis and MDRO colonization and infection in SOT patients.

RECENT FINDINGS: Recent studies have added complementary metagenomics, internal transcribed spacer sequencing, metabolomics, and pathway analysis to descriptive microbiome profiling. Enhanced ecologic frameworks have identified microbial, functional, and clinical signatures associated with MDRO colonization and infection. Microbiome-targeting interventions are emerging as strategies to reduce morbidity associated with MDRO infection.

SUMMARY: MDRO infection is a significant cause of post-transplant mortality. Persistent gut dysbiosis peri-transplant reduces colonization resistance and predisposes patients to adverse clinical outcomes. Understanding the dynamics of this process will aid in the care of these high-risk patients.},
}

Humans
*Dysbiosis/microbiology/immunology
*Organ Transplantation/adverse effects/mortality
Risk Factors
*Gastrointestinal Microbiome/drug effects
*Drug Resistance, Multiple, Bacterial
Treatment Outcome
*Anti-Bacterial Agents/therapeutic use/adverse effects
Host-Pathogen Interactions
*Bacteria/drug effects/pathogenicity
Animals
*Bacterial Infections/microbiology/drug therapy/immunology

@article {pmid42517626,
year = {2026},
author = {Price, DC and Bezhani, FL and Meng, Z and Porfirio-LaStrapes, M and Wagner, NE and Javanmard, M and Han, T and Barnes, MM},
title = {Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0093826},
pmid = {42517626},
issn = {2165-0497},
support = {1R21AI159459 - 01/NH/NIH HHS/United States ; AMCARF 2018-01//American Mosquito Control Association/ ; Multistate NE1943//United States Department of Agriculture/ ; },
mesh = {Animals ; *Virome/genetics ; *Feces/virology ; *Culex/virology ; *RNA Viruses/genetics/isolation & purification/classification ; Metagenomics/methods ; *Mosquito Vectors/virology ; North America ; Humans ; RNA, Viral/genetics ; Female ; *Culicidae/virology ; },
abstract = {Nearly 30% of emerging infectious disease events worldwide are transmitted by arthropod vectors, and this proportion continues to rise. Rapid and accurate detection is critical for directing vector control interventions, thereby reducing the likelihood of widespread transmission. Surveillance of infected mosquitoes can provide an early warning of impending human infection; however, conventional virus testing relies on processing large pools of mosquitoes and requires labor-intensive pre-processing. During rapidly developing epidemic or panzootic events, these delays may limit the effectiveness of public health responses. Mosquito excreta has recently emerged as a promising alternative substrate for pathogen detection. Sugar-fed mosquitoes regularly excrete gut contents, offering a rich source of nucleic acids. In this study, we developed and applied custom superhydrophobic excreta-collection funnels that efficiently aggregate excreta produced by field-collected Culex mosquitoes into attached microcentrifuge tubes. Shotgun metagenomic sequencing of this material revealed a diverse RNA virome, including both globally distributed viruses and those reported here for the first time from the Americas. Beyond virus detection, additional analyses enabled confirmation of host mosquito species and identification of trypanosomatid parasites, demonstrating the broader utility of mosquito excreta for integrated surveillance. We anticipate that methods and devices of this type will become valuable components of vector surveillance programs, particularly in remote or resource-limited settings where repeated collections are challenging. Overall, our findings highlight the potential of excreta-based monitoring to improve early detection of emerging or unknown pathogens of One Health importance, refine our understanding of mosquito virome biogeography, and facilitate the discovery of previously undescribed viruses.IMPORTANCEMany infectious diseases that affect people and animals are spread by mosquitoes and other biting insects, and the number of these outbreaks is increasing. Detecting pathogens in mosquito populations early can provide a critical warning before human cases begin, allowing health officials to act quickly. However, traditional surveillance requires collecting and processing large numbers of mosquitoes, which can be slow and labor-intensive during fast-moving outbreaks. Here we demonstrate a simpler approach: testing mosquito waste. When mosquitoes feed on sugar, they excrete material that contains genetic traces of viruses and other organisms. Using specially designed collection devices and modern genetic sequencing, we show that mosquito excreta can reveal a wide range of viruses and parasites while also identifying the mosquito species present. This method could make disease surveillance faster and more practical in remote or resource-limited settings, improving our ability to detect emerging pathogens that threaten human, animal, and environmental health.},
}

Animals
*Virome/genetics
*Feces/virology
*Culex/virology
*RNA Viruses/genetics/isolation & purification/classification
Metagenomics/methods
*Mosquito Vectors/virology
North America
Humans
RNA, Viral/genetics
Female
*Culicidae/virology

@article {pmid42545016,
year = {2026},
author = {Seo, Y and Kim, J and Yeom, M and Park, S-Y and Lee, S and Ahn, S and Hahm, D-H and Kim, K and Kwon, S-K and Park, H-J},
title = {Gut microbiota contributes to the therapeutic effect of acupuncture in atopic dermatitis.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0391225},
pmid = {42545016},
issn = {2165-0497},
support = {RS-2023-00211512//National Research Foundation of Korea/ ; RS-2024-00409969//National Research Foundation of Korea/ ; },
mesh = {*Dermatitis, Atopic/therapy/microbiology ; Humans ; Animals ; *Acupuncture Therapy/methods ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Mice ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Disease Models, Animal ; Treatment Outcome ; Adult ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; },
abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a central regulator of immune homeostasis, metabolic balance, and therapeutic outcomes. Atopic dermatitis (AD), a chronic inflammatory skin disease, is closely linked to gut microbial dysbiosis. Traditionally regarded as a neurostimulatory therapy, acupuncture (Acu) has demonstrated increasing efficacy in alleviating AD symptoms and improving gastrointestinal function. These observations suggest that the therapeutic effects of Acu in AD may be mediated, in part, by modulation of the gut microbiome. In this study, AD patients were stratified into responder (R) and non-responder (NR) groups based on clinical improvement. Gut microbiome profiling revealed that R patients exhibited greater microbial diversity and compositional stability, indicative of a more balanced gut ecosystem. Specific taxa, including Alistipes ihumii and Odoribacter splanchnicus, were enriched in R individuals and may serve as microbial predictors of treatment responsiveness. Importantly, fecal microbiota transplantation (FMT) from R donors restored Acu efficacy in a mouse model of AD, whereas FMT from NR donors did not. These findings support the gut-skin axis and highlight the integral role of the gut microbiome in mediating the therapeutic effects of Acu for AD, suggesting potential for microbiome-based personalized treatment.

IMPORTANCE: Increasing evidence supports the gut microbiome's role in modulating treatment responses in atopic dermatitis (AD), but direct evidence linking acupuncture efficacy with microbiome composition has been lacking. Previous studies did not assess causal relationships via fecal microbiota transplantation (FMT) or functional metagenomics. This study identifies specific gut microbes associated with acupuncture response in AD and confirms their causal role using FMT. It also links functional metabolic pathways to therapeutic efficacy, offering a mechanism-based insight. Our findings support microbiome-informed personalized acupuncture approaches for AD and suggest gut microbiota as a therapeutic modulator in neuroimmune regulation.

CLINICAL TRIALS: This study was registered in the Korean Clinical Trial Registry (CRIS, registration number: KCT0005422).},
}

*Dermatitis, Atopic/therapy/microbiology
Humans
Animals
*Acupuncture Therapy/methods
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/physiology
Mice
Female
Bacteria/classification/genetics/isolation & purification
Male
Disease Models, Animal
Treatment Outcome
Adult
Feces/microbiology
Dysbiosis/therapy/microbiology

@article {pmid42578670,
year = {2026},
author = {Li, Z and Sun, J and Yang, J and Han, P and Min, L and Cheng, Y and Zou, Y and Liu, Z},
title = {Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0315324},
pmid = {42578670},
issn = {2165-0497},
mesh = {Humans ; *Bacteroides/genetics/isolation & purification/classification/physiology ; Metagenomics ; Feces/microbiology ; *Depression/microbiology ; Metagenome ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Nitric Oxide/metabolism/biosynthesis ; },
abstract = {Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.},
}

Humans
*Bacteroides/genetics/isolation & purification/classification/physiology
Metagenomics
Feces/microbiology
*Depression/microbiology
Metagenome
Female
Male
*Gastrointestinal Microbiome
Adult
Middle Aged
Nitric Oxide/metabolism/biosynthesis

@article {pmid42578673,
year = {2026},
author = {Mirăuță, B and Riza, A-L and Streata, I and Pirvu, A and Dorobantu, S and Dragos, A and Surleac, M and Netea, MG},
title = {Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0052826},
pmid = {42578673},
issn = {2165-0497},
support = {PN-IV-P6-6.1-CoEx-2024-0196 (17CoEx/2026)//Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI)/ ; PNRR/2022/C9/MCID/I8, Contract No. 760057/23.05.2023//Ministry of Research, Innovation and Digitalization, Romania - National Recovery and Resilience Plan (PNRR), Pillar III, Component 9, Investment I8/ ; P_37_745, MySMIS 103454, Contract No. 31/01.09.2016//Ministry of European Funds, Romania - Competitiveness Operational Programme/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Romania ; Metagenomics ; Feces/microbiology ; },
abstract = {The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favorable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. This first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort, a population underrepresented in microbiome studies and characterized by high antibiotic consumption, addresses a gap in current microbiome research. We report an enrichment of Enterobacteriaceae although overall composition is more comparable to other European than non-European cohorts. Community configurations align with established enterotype patterns, and our analysis provides insight into their relationship with within-phylum diversity. The analysis of antimicrobial resistance provides insight into the prevalence of resistance genes within this reservoir. We specifically report the presence of cfr(E), a Clostridioides difficile gene, and tet(X5), a variant from the ubiquitous tet family, genes not previously reported in healthy European populations. Integration with data from the European Centre for Disease Prevention and Control links the overall prevalence of resistance genes in this reservoir to antibiotic classes with higher community consumption in this population, notably beta-lactams and quinolones, highlighting potential targets for antibiotic stewardship programs. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify potential immune-priming roles for Collinsella, Flavonifractor, and Bifidobacterium species.IMPORTANCEThis first comprehensive study of the healthy gut microbiome in a Romanian cohort addresses a gap in current microbiome research, dominated by data sets from a limited number of regions. It sets a baseline for the microbiome and resistome composition of this population, and, while definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such study helps contextualize future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes and the concordance with commonly used antibiotics in the community reinforce the need to address antibiotic use in public health strategies. Although gut microbiome-immunity relationships remain incompletely understood, our findings support a role for microbiome composition in immune-related traits and provide a valuable resource for future studies.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Romania
Metagenomics
Feces/microbiology

@article {pmid42584065,
year = {2026},
author = {Roush, C and Whiteley, M},
title = {Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0182026},
pmid = {42584065},
issn = {2165-0497},
support = {R01 DE023193/DE/NIDCR NIH HHS/United States ; R01DE020100/DE/NIDCR NIH HHS/United States ; R01DE023193/DE/NIDCR NIH HHS/United States ; },
mesh = {*Bacteriophages/genetics/classification/isolation & purification ; *Wastewater/virology/microbiology ; Humans ; Genome, Viral ; *Mouth/virology/microbiology ; Metagenomics ; Microbiota ; *Bacteria/virology/classification/genetics ; Metagenome ; Phylogeny ; Tannerella forsythia/virology ; Porphyromonas gingivalis/virology ; },
abstract = {Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.},
}

*Bacteriophages/genetics/classification/isolation & purification
*Wastewater/virology/microbiology
Humans
Genome, Viral
*Mouth/virology/microbiology
Metagenomics
Microbiota
*Bacteria/virology/classification/genetics
Metagenome
Phylogeny
Tannerella forsythia/virology
Porphyromonas gingivalis/virology

@article {pmid42680742,
year = {2026},
author = {Low, A and Yang, Z and Anantaya, KT and Zhao, S and Tan, WC and Perez, RL and Chung The, H and Lim, SZY and Liu, L and Gounot, JS and Kwah, JS and Ong, RT and Nagarajan, N and Lee, JWJ and Mo, Y},
title = {Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42680742},
issn = {2041-1723},
mesh = {Humans ; *Escherichia coli/genetics/isolation & purification/classification ; *Escherichia coli Infections/microbiology/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metagenomics ; *Carrier State/microbiology ; Asia, Southeastern/epidemiology ; Intestines/microbiology ; },
abstract = {Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.},
}

Humans
*Escherichia coli/genetics/isolation & purification/classification
*Escherichia coli Infections/microbiology/epidemiology
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Cohort Studies
Metagenomics
*Carrier State/microbiology
Asia, Southeastern/epidemiology
Intestines/microbiology

@article {pmid42683728,
year = {2026},
author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G},
title = {Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725403},
doi = {10.1080/19490976.2026.2725403},
pmid = {42683728},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Metagenome ; Mice ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Feces/microbiology ; Irritable Bowel Syndrome/therapy/microbiology ; Computer Simulation ; },
abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remain limited, in part because the role of donor‒recipient metabolic interactions in shaping the post-FMT community remains poorly understood. Here, we leverage metagenome-scale metabolic modeling to quantify metabolic niche complementarity between donor and recipient microbiomes and predict post-FMT community composition. Using MICOM-derived metabolic models, we show that donor genomes whose metabolic flux profiles are more dissimilar from the recipient community colonize at significantly higher rates in a murine FMT model. In a human IBS trial, the same metric predicted post-FMT community composition via leave-one-out cross-validation and captured known disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to evaluate personalized donor screening, identifying super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition. Together, these results support metabolic niche complementarity as a potential determinant of post-FMT community composition and provide a mechanistic basis for evaluating donor-recipient metabolic compatibility. This framework offers a scalable approach for generating testable hypotheses for personalized donor selection.},
}

*Fecal Microbiota Transplantation
Humans
Animals
*Metagenome
Mice
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Feces/microbiology
Irritable Bowel Syndrome/therapy/microbiology
Computer Simulation

@article {pmid42685266,
year = {2026},
author = {Colajanni, A and Uricaru, R and Darko, S and Subramanian, R and Douek, DC and Thiébaut, R and Thebault, P},
title = {Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag454},
pmid = {42685266},
issn = {1477-4054},
mesh = {Humans ; *Microbiota/genetics ; Benchmarking ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; },
abstract = {Human RNA sequencing (RNA-seq) data originally generated for human transcriptome profiling are overwhelmingly dominated by host sequences, yet they often contain a small fraction of non-human reads that can be exploited for microbial detection. When such datasets are repurposed for secondary microbiome-oriented analyses, extracting and accurately classifying this weak microbial signal becomes technically challenging, and no ready-to-use pipeline currently exists. In this study, we evaluate computational strategies for filtering host reads and classifying microbial transcripts in host-dominated RNA sequencing data. We compare assembly-based approaches similar to those used in a previous study focusing on microbial translocation with state-of-the-art assembly-free methods, and assess their respective strengths and limitations using simulated datasets reflecting low microbial abundance. Our results show that assembly-based methods yield accurate taxonomic predictions but struggle at low read depth, whereas assembly-free methods are more robust in sparse settings at the cost of reduced precision. To leverage the complementarity of both approaches, we propose a hybrid pipeline that integrates assembly-based and assembly-free classification. On simulated data, this hybrid strategy improves microbial classification performance compared with either approach alone. Application to a real human metatranscriptomic dataset analyzed in a microbial translocation context illustrates the broader microbial signal captured by the hybrid approach, despite intrinsic challenges related to the absence of reliable ground truth and the risk of host read misclassification. Our work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.},
}

Humans
*Microbiota/genetics
Benchmarking
*Transcriptome
*Gene Expression Profiling/methods
Sequence Analysis, RNA/methods
*Computational Biology/methods

@article {pmid42252320,
year = {2026},
author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W},
title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42252320},
issn = {2045-2322},
support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; },
mesh = {Humans ; *Gout/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Dysbiosis/microbiology ; Bacteria/genetics/classification ; Biodiversity ; },
abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.},
}

Humans
*Gout/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Metagenome
*Dysbiosis/microbiology
Bacteria/genetics/classification
Biodiversity

@article {pmid42296622,
year = {2026},
author = {Pravara, R and Praveen, R and Seema, B},
title = {Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {60},
number = {},
pages = {101902},
doi = {10.1016/j.cbd.2026.101902},
pmid = {42296622},
issn = {1878-0407},
mesh = {Animals ; Symbiosis ; *Microbiota ; *Gossypium/parasitology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Hemiptera/microbiology/growth & development ; },
abstract = {BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus.

RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism.

CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.},
}

Animals
Symbiosis
*Microbiota
*Gossypium/parasitology
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Hemiptera/microbiology/growth & development

@article {pmid42497006,
year = {2026},
author = {Arjunan, S and Pemberton, I and Li, XS and Sangwan, N and Akino, L and Opoku, E and Verbovetskiy, D and Nemet, I and Kim, HS and Masumiya, H and Wang, Z and Lupica, JA and Tian, MY and Mao, K and Mallela, DP and Mohan, ML and Schumacher, SM and Rennison, JH and Prasad, SVN and Laurita, KR and Chodisetty, V and Chung, MK and Van Wagoner, DR and Barnard, J and Smith, JD and Wazni, O and Hazen, SL and Koeth, RA},
title = {Gut microbial trimethylamine N-oxide generation promotes risk of atrial fibrillation via muscarinic receptor-mediated autonomic dysfunction.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {17},
pages = {},
pmid = {42497006},
issn = {1558-8238},
mesh = {Animals ; *Methylamines/metabolism ; *Atrial Fibrillation/metabolism/microbiology/physiopathology/genetics/pathology ; Humans ; Mice ; *Gastrointestinal Microbiome ; *Receptors, Muscarinic/metabolism/genetics ; Male ; Female ; Mice, Inbred C57BL ; Choline/pharmacology/analogs & derivatives ; Mice, Transgenic ; Middle Aged ; Aged ; Cyclic AMP Response Element Modulator/genetics/metabolism ; },
abstract = {Gut microbiota-derived trimethylamine N-oxide (TMAO) plays a role in the pathogenesis of cardiovascular disease, but its role in the pathogenesis of atrial fibrillation (AF) remains uncertain. TMAO levels were quantified in plasma from serial subjects undergoing elective cardiac catheterizations and shown to independently associate with prevalent AF following adjustment for risk factors. Human cAMP response element modulator isoform IbΔC-X transgenic mice (CREM-IbΔC-X) supplemented with a TMAO diet developed AF sooner. C57BL/6J mice on and off a TMAO diet had more inducible AF via a transesophageal pacing study compared with chow-fed controls. Dietary choline supplementation increased circulating TMAO levels and significantly accelerated AF onset in CREM-IbΔC-X mice. Iodomethylcholine (IMC) reduced circulating TMAO levels and choline-induced AF onset. Cecal metagenomic analyses showed that choline supplementation induced changes in microbial communities associated with AF, while many of these changes were attenuated by IMC. Choline supplementation promoted overall adverse atrial remodeling with left atrial dilation. Optical mapping studies showed that mice supplemented with choline exhibited reduced conduction velocity, shortened action potential duration at 80% repolarization, and decreased wavelength. TMAO inhibited muscarinic receptor 2, resulting in autonomic dysfunction that promotes AF. In summary, TMAO, independently associated with AF risk in subjects, enhanced AF in multiple mouse models via autonomic dysfunction and is a therapeutic target for preventing AF.},
}

Animals
*Methylamines/metabolism
*Atrial Fibrillation/metabolism/microbiology/physiopathology/genetics/pathology
Humans
Mice
*Gastrointestinal Microbiome
*Receptors, Muscarinic/metabolism/genetics
Male
Female
Mice, Inbred C57BL
Choline/pharmacology/analogs & derivatives
Mice, Transgenic
Middle Aged
Aged
Cyclic AMP Response Element Modulator/genetics/metabolism

@article {pmid42675564,
year = {2026},
author = {Akyol, CK and Bilaç, Ö and Çam, FS},
title = {Does the Gut Microbiota Play a Role in Attention-Deficit/Hyperactivity Disorder in Childhood? A Pilot Study From Turkey.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70057},
doi = {10.1002/dneu.70057},
pmid = {42675564},
issn = {1932-846X},
support = {2022-146//Manisa Celal Bayar University Scientific Research Projects Coordination Unit/ ; },
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology ; Male ; Pilot Projects ; *Gastrointestinal Microbiome/physiology ; Turkey ; Female ; Child ; Feeding Behavior/physiology ; Sleep/physiology ; },
abstract = {The pathophysiology of attention-deficit/hyperactivity disorder (ADHD) is not fully understood, but increasing evidence suggests that gut microbiota may play a role. This study compared the gut microbiota of children with ADHD with that of a control group of healthy children, and examined their dietary and sleep habits. Ten medication-naïve children aged 612 years who had recently been diagnosed with ADHD and ten healthy controls were included. ADHD diagnoses were confirmed using the Schedule for Affective Disorders and Schizophrenia for School-Age ChildrenPresent and Lifetime Version (K-SADS-PL). Sleep and eating habits were assessed using the 2nd Level Sleep Disorder Short Form, the Children's Eating Behaviour Inventory, and a form to collect sociodemographic and clinical information. The gut microbiota were analysed using 16S NGS metagenome analysis. A significant decrease in the Shannon and Simpson diversity index values was observed in the ADHD group compared to the control group. Despite the presence of a percentage difference, no statistically significant differences were observed between the groups with respect to species, genus, family, order, class or phylum. Following evaluation of the sleep and eating habit scale scores, no statistically significant difference between the groups was determined.These findings suggests that children with ADHD may alter gut microbiota diversity.However, the absence of significant taxonomic differences and the small sample size mean that these results should be interpreted with caution. Further, larger, adequately powered studies are needed to validate these findings and clarify the potential role of gut microbiota in the pathophysiology of ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology
Male
Pilot Projects
*Gastrointestinal Microbiome/physiology
Turkey
Female
Child
Feeding Behavior/physiology
Sleep/physiology

@article {pmid42675742,
year = {2026},
author = {Shaikh, SS and Malek, F},
title = {Healthy subjects gut microbiome modulation by Bacillus coagulans BCP92: A randomized, double-blind, placebo-controlled clinical trial.},
journal = {Medicine},
volume = {105},
number = {35},
pages = {e50435},
doi = {10.1097/MD.0000000000050435},
pmid = {42675742},
issn = {1536-5964},
mesh = {Humans ; *Probiotics/administration & dosage ; *Bacillus coagulans/physiology ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Male ; Adult ; Fatty Acids, Volatile/analysis/metabolism ; Female ; Healthy Volunteers ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: Probiotics are recognized for their ability to restore balance in the gut microbiome during dysbiosis. However, their effects on the gut microbiota of healthy individuals have rarely been investigated. This study aimed to evaluate the safety and efficacy of Bacillus coagulans (Heyndrickxia coagulans) BCP92 and its influence on microbiota composition in healthy subjects.

METHODS: In the present investigation, healthy participants (n = 48) were allocated into 2 groups and administered either Bacillus coagulans BCP92 capsules (1 billion CFU/capsule) or a placebo containing maltodextrin for 42 days. Microbiome composition and short-chain fatty acid analyses were subsequently conducted.

RESULTS: Analysis of metagenomes showed no major alterations in gut microbiome composition among participants who received B. coagulans BCP92 supplementation. However, subtle beneficial changes were observed in the treatment group, suggesting that probiotic administration may increase advantageous phyla, classes, orders, families, and some genera, while decreasing potentially harmful groups. A slight increase in short-chain fatty acids (SCFA) was also observed in the fecal samples.

CONCLUSIONS: This study implies that extended supplementation with the probiotic B. coagulans BCP92 may lead to substantial improvements in gut microbiome composition and SCFA levels.},
}

Humans
*Probiotics/administration & dosage
*Bacillus coagulans/physiology
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Feces/microbiology/chemistry
Male
Adult
Fatty Acids, Volatile/analysis/metabolism
Female
Healthy Volunteers
Young Adult
Metagenome

@article {pmid42677031,
year = {2026},
author = {Ceja-Navarro, JA and Patel, D and Genco, G and Byer, A and Ning, D and Wan, KH and Celniker, SE and Zhou, J and Dijkstra, P and Hungate, BA and Pett-Ridge, J and Brodie, EL},
title = {Ecosystem retrogression enhances cross-domain microbial stability and increases the genetic potential for nutrient cycling.},
journal = {mLife},
volume = {5},
number = {4},
pages = {486-506},
pmid = {42677031},
issn = {2770-100X},
abstract = {Ecosystem retrogression drives nutrient depletion, reduced productivity, and profound reorganization of soil microbial communities. Using amplicon sequencing and genome-resolved metagenomics, we examined how cross-domain microbial networks and functional gene potential respond to long-term phosphorus and nitrogen limitation along the well-characterized Ecological Staircase chronosequence in Mendocino, California, USA. Microbial diversity and abundance declined sharply with terrace age for prokaryotes, predatory protists, and bacteriophages, whereas fungi and phototrophic protists increased in nutrient-depleted, acidic soils. These compositional shifts were accompanied by major changes in reconstructed microbial networks: relative modularity increased alongside robustness, indicating adaptive reorganization that may sustain ecosystem function under resource scarcity. Fungi emerged as central stabilizers in these restructured networks, carrying enriched genetic potential to degrade plant polymers and mobilize phosphorus and nitrogen. Despite a decline in overall phage diversity, the relative abundance of phages encoding phosphorus-mobilizing auxiliary metabolic genes increased, suggesting that viral contributions to host phosphorus metabolism may be enhanced under nutrient limitation. Together, these results demonstrate that ecosystem retrogression drives cross-domain microbial reorganization toward fewer but more interconnected lineages, characterized by greater integration of functional genetic potential. This reorganization enhances the potential for functional resilience under extreme nutrient limitation, revealing how microbial networks adapt to maintain the capacity for nutrient cycling and stability as soils age and fertility declines.},
}

@article {pmid42677827,
year = {2026},
author = {Chen, K and Yang, Z and Peng, J and Liu, C and Yu, Y and Cai, X and Liu, B and Li, S and Chen, T and Jung, S and Tian, Y and Xu, Q and Rao, X and Wu, Z and Wang, H and Di, Y and Wang, L and Wang, J and Lee, MS and Zou, Y and He, N and Li, S},
title = {Bacteroides cellulosilyticus-derived 2-hydroxyphenylacetic acid rectifies hepatic lipid homeostasis in MASLD by targeting the PPARγ-CD36 axis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725392},
doi = {10.1080/19490976.2026.2725392},
pmid = {42677827},
issn = {1949-0984},
mesh = {*PPAR gamma/metabolism/genetics ; *CD36 Antigens/metabolism/genetics ; Humans ; *Phenylacetates/metabolism ; *Lipid Metabolism/drug effects ; Homeostasis ; *Fatty Liver/metabolism/microbiology ; *Bacteroides/metabolism ; *Liver/metabolism ; Hepatocytes/metabolism ; Signal Transduction/drug effects ; Gastrointestinal Microbiome ; },
abstract = {The gut microbiota plays an important role in the occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD), but the specific molecular mechanisms involved have not been fully elucidated. In this study, human cohort studies were performed to identify that the relative abundance of Bacteroides cellulosilyticus (B. cellulosilyticus) was significantly decreased in patients with MASLD. Through the integration of metagenomic and metabolomic analyses, it was confirmed that B. cellulosilyticus and its metabolite 2-hydroxyphenylacetic acid (2HPAA) are key factors regulating the occurrence and development of MASLD. Single-cell sequencing and lipidomic analyses revealed that 2HPAA can enter the liver through the enterohepatic circulation to exert regulatory effects. Specifically, 2HPAA inhibits the peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway, thereby suppressing the expression of the fatty acid transporter CD36. Meanwhile, 2HPAA regulates lipid metabolism in hepatocytes by significantly enhancing palmitate conversion efficiency and inhibiting CD36 palmitoylation. This dual regulatory effect on CD36 expression and palmitoylation can reduce lipid accumulation in hepatocytes and ultimately alleviate MASLD progression. These findings reveal the mechanism by which B. cellulosilyticus and 2HPAA alleviate MASLD by targeting the PPARγ-CD36 pathway. This work provides a new perspective for the study of gut microbiota-host interactions in regulating liver diseases.},
}

*PPAR gamma/metabolism/genetics
*CD36 Antigens/metabolism/genetics
Humans
*Phenylacetates/metabolism
*Lipid Metabolism/drug effects
Homeostasis
*Fatty Liver/metabolism/microbiology
*Bacteroides/metabolism
*Liver/metabolism
Hepatocytes/metabolism
Signal Transduction/drug effects
Gastrointestinal Microbiome

@article {pmid42680271,
year = {2026},
author = {Zhu, D and Xie, J and Li, P and Mei, J},
title = {Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {119937},
doi = {10.1016/j.foodres.2026.119937},
pmid = {42680271},
issn = {1873-7145},
mesh = {*Multiomics ; *Food Microbiology/methods ; *Artificial Intelligence ; *Food Preservation/methods ; *Microbiota ; Metabolomics ; Metagenomics ; },
abstract = {In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.},
}

*Multiomics
*Food Microbiology/methods
*Artificial Intelligence
*Food Preservation/methods
*Microbiota
Metabolomics
Metagenomics

@article {pmid42680349,
year = {2026},
author = {Li, S and Zhang, H and Yang, Y and Xia, Y and Ni, B and Ai, L},
title = {Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {120059},
doi = {10.1016/j.foodres.2026.120059},
pmid = {42680349},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; *Food Microbiology ; Bacteria/metabolism/genetics/classification ; Metabolomics ; *Fermented Foods/microbiology/analysis ; Metagenomics ; Ethanol/analysis ; },
abstract = {Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.},
}

*Volatile Organic Compounds/analysis/metabolism
Fermentation
*Alcoholic Beverages/microbiology/analysis
*Microbiota
Gas Chromatography-Mass Spectrometry
*Food Microbiology
Bacteria/metabolism/genetics/classification
Metabolomics
*Fermented Foods/microbiology/analysis
Metagenomics
Ethanol/analysis