@article {pmid41715233,
year = {2026},
author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL},
title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {72},
pmid = {41715233},
issn = {2049-2618},
support = {Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; },
mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; },
abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.

RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.},
}

Metagenome
*Rumen/enzymology/microbiology
Animals
*Cattle/microbiology
Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Fatty Acids, Volatile/biosynthesis
*Methane/biosynthesis
Hydrogen/metabolism
Metabolic Networks and Pathways/drug effects

@article {pmid41715225,
year = {2026},
author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M},
title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02332-2},
pmid = {41715225},
issn = {2049-2618},
abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.

METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.

RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.

CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.},
}

@article {pmid41715166,
year = {2026},
author = {Zhang, J and Xu, L and Ge, X and Zi, X and Chen, S and Liu, C and Wang, K and Zhou, J and Dou, T and Wong, JWC and Lin, Q and Kang, X and Cao, Z},
title = {Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02347-3},
pmid = {41715166},
issn = {2049-2618},
support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 202401AU070079//Yunnan Fundamental Research Projects/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; 202301BD070001-136//Key Project of Yunnan Province Agricultural Joint Special Project/ ; 202305AC160040//Yunnan Province Young and Middle-aged Academic and Technical Leader Reserve Talent Project/ ; },
abstract = {BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.

RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.

CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.},
}

@article {pmid41714980,
year = {2026},
author = {Ceylani, T and Teker, HT and Önlü, H and Ünver, T and Allahverdi, H and Şahin, E and Atalan, E},
title = {Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12650-w},
pmid = {41714980},
issn = {1471-2164},
support = {FOA-2024-3587//Inönü University Scientific Research Projects Coordination Unit (BAP)/ ; },
}

@article {pmid41714786,
year = {2026},
author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S},
title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40561-z},
pmid = {41714786},
issn = {2045-2322},
}

@article {pmid41714781,
year = {2026},
author = {Su, JW and Elsheikha, HM and Guo, L and Liu, R and Shang, KM and Yu, HL and Ma, H and Ni, HB and Chen, BN and Zhang, XX and Yang, X},
title = {Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09726-4},
pmid = {41714781},
issn = {2399-3642},
support = {2022KJ169//Department of Education of Shandong Province (Department of Education, Shandong Province)/ ; },
abstract = {The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.},
}

@article {pmid41714776,
year = {2026},
author = {Balázs, B and Boros, Á and Pankovics, P and Mátics, R and Urbán, P and Herczeg, R and Knowles, NJ and Reuter, G},
title = {Genetic characterization of two novel picornaviruses from birds, white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39780-1},
pmid = {41714776},
issn = {2045-2322},
abstract = {In this study, two novel picornaviruses (eagle/WE6/HUN/2014, PV454551-PV454552 and avocet/PA12/HUN/2018, PV454553) were detected in white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary, and characterized by next generation sequencing, RT-PCR and Sanger sequencing methods. The complete polyprotein coding genomes were 6,573 and 6,567 nt long and had the genome organization 5'UTR[IRES-III]-[VP4-VP2-VP3-VP1-2A-2B-2C[hel]-3A-3B[VPg]-3C[pro]-3D[pol]]-3'UTR-poly(A)n. The P1 and the 3C[pro] proteins of the eagle/WE6/HUN/2014 showed 47.9% and 62.4% aa sequence identities to the corresponding proteins of the picornavirus (MT138036) from a little egret metagenome, respectively. The 2C[hel]/3D[pol] had 44.1%/41% aa identity to the corresponding proteins of bat-origin picornaviruses (OR867633 and KX420952). The P1 protein of the avocet/PA12/HUN/2018 had 53% aa sequence identity to the P1 protein of crane70contig328 (OQ423840) from red-crowned crane metagenome; the 2C[hel], 3C[pro] proteins had 52.6%, 52.3% aa sequence identity to the corresponding proteins of picornavirus (MT138035) from bird metagenome and 3D[pol] had 43.2% aa identity to the 3D[pol] of the picornavirus (MT138036) from a little egret metagenome, respectively. The 3'UTR of avocet/PA12/HUN/2018 contained two repetitive nt sequence motifs (the 17-nt-long Motif-1 at five times forming a secondary RNA structure and the 9-nt-long Motif-2 at two times). The eagle/WE6/HUN/2014 and avocet/PA12/HUN/2019 represent the founding members of two potential novel bird-origin picornavirus species and even genera in the subfamily Heptrevirinae (family Picornaviridae).},
}

@article {pmid41714186,
year = {2026},
author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W},
title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag037},
pmid = {41714186},
issn = {1751-7370},
abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.},
}

@article {pmid41713817,
year = {2026},
author = {Zhao, Q and Cao, Y and Zhang, Z and Yang, Y and Wang, L and Xu, M and Mao, Y and Zhang, X and Zeng, M and Yang, P and Chen, Q and Yan, H and Yang, G},
title = {Xiao-Chaihu-Tang preserves intestinal barrier and ameliorates irinotecan-evoked delayed diarrhea by anchoring endogenous tryptophol to modulate inflammation and oxidation dependent on AhR-UGT1A1-microbiota axis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121380},
doi = {10.1016/j.jep.2026.121380},
pmid = {41713817},
issn = {1872-7573},
abstract = {Xiao-Chaihu-Tang (XCHT), a well-known traditional formula, is commonly used to treat various types of diarrhea. It also exhibits promising efficacy against chemotherapy irinotecan (CPT-11)-induced delayed diarrhea (DD). However, its underlying mechanisms, specifically concerning endogenous metabolites, key pathways, and functional gut bacteria at the species level, remain unclear, severely restricting its clinical application.

AIM OF THE STUDY: This study aimed to elucidate the biomarkers, pathways, and functional bacteria involved in XCHT's alleviating CPT-11-evoked DD using multi-omics approaches, antagonists, and fecal microbiota transplantation (FMT).

MATERIALS AND METHODS: First, the ingredients of XCHT and absorbed compounds in rat plasma were identified using liquid chromatography-mass spectrometry (LC-MS). Next, the therapeutic effects of XCHT were assessed by monitoring perianal status, body weight, disease activity index, food and water intake, and histopathological changes in the colon (hematoxylin and eosin, alcian blue-periodic acid-schiff staining). The underlying mechanisms were studied using metabolomics and network pharmacology, which highlighted the role of endogenous biomarkers and associated pathways. Tryptophol was identified as a key correlate, and its efficacy was further validated in rat and Caco-2 models using antagonists of potential targets (AhR and UGT1A1). The levels of inflammatory cytokines, and oxidative stress markers, intestinal barrier proteins, and mucins were detected by enzyme-linked immunosorbent assay (ELISA), Western blotting, and immunofluorescence. Furthermore, functional gut bacteria were identified using metagenomic sequencing and validated using FMT, while gut leakage was detected using fluorescence in situ hybridization (FISH). Finally, the interactions between tryptophol with targets of AhR and UGT1A1 were examined using molecular docking, molecular dynamics, and surface plasmon resonance.

RESULTS: LC-MS analysis identified 43 phytochemicals in XCHT and 17 compounds absorbed in plasma. XCHT, similar to tryptophol, attenuated DD by improving perianal status, disease activity index, and colon pathology, while increasing body weight, food intake, and water intake. Metabolomics analysis revealed 33 potential endogenous biomarkers, including PGB3, LysoPA, and so on. Integrated with network pharmacology, the results indicated that the therapeutic effect of XCHT involved the regulation of tryptophan metabolism, arachidonic acid metabolism, inflammation, and oxidative stress. Tryptophol, which exhibited a strong correlation with efficacy indices, reduced inflammation and oxidation in vivo/vitro, and enhanced intestinal barrier protein and mucin expression in an AhR-UGT1A1-dependent manner. Furthermore, metagenomic sequencing and FISH demonstrated that both XCHT and tryptophol normalized the abundance of 10 gut bacterial species (for example, Lactobacillaceae bacterium, Massiliimalia timonensis, and Limosilactobacillus reuteri) and inhibited bacterial invasion. Molecular interaction studies confirmed the strong binding between tryptophol with AhR and UGT1A1.

CONCLUSION: This study demonstrates that XCHT preserves intestinal barrier integrity in rats and alleviates CPT-11-induced DD. This protective effect is mediated by modulating inflammation and oxidative stress via the tryptophol- AhR-UGT1A1-microbiota axis, providing a novel paradigm for mechanistic studies on toxicity reduction in clinical chemotherapy drugs.},
}

@article {pmid41713744,
year = {2026},
author = {Pierre, L and Alain, LR and Carole, F and Houée, P and Patricia, LG and Hirchaud, E and Christophe, S and Arnaud, B},
title = {Longitudinal analysis of surface-associated bacterial ecology and resistome dynamics in a pig slaughterhouse.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100724},
doi = {10.1016/j.jfp.2026.100724},
pmid = {41713744},
issn = {1944-9097},
abstract = {Slaughterhouses constitute key stages for the transmission of bacterial pathogens and antimicrobial resistance throughout the meat production chain, with significant implications for food safety. This study investigated the bacterial communities and resistome profiles of surface-associated microbes in a pig slaughterhouse sampled at two-year intervals in 2017 and 2019. Thirty-five strain of Salmonella enterica serovar Typhimurium and its monophasic variant, major pathogenic serovars of the sector, were collected through the slaughtering line in this time frame, and they displayed multidrug resistance profiles characteristic of the pig sector. Whole-genome analysis revealed no clear phylogenetic clustering by site or sampling date. Both 16S rRNA metabarcoding and shotgun metagenomics underlined site-specific bacterial communities dominated by Moraxellaceae family and with a relative stable composition across the sampling period. The upstream of the slaughtering line (dehairing stage) was characterized by aminoglycoside and tetracycline resistance genes, predominantly associated with Acinetobacter, Escherichia, and Clostridium, alongside oxidative stress genes carried by Streptococcus. At the downstream section of the slaughtering process, the red offal platform exhibited increased diversity and abundance of antibiotic and biocide resistance determinants. These included β-lactam and carbapenem resistance genes as well as efflux pump-associated elements (adeJ), mainly linked to Acinetobacter which was consistently enriched suggesting its potential role as a reservoir for resistance genes. Overall, these findings provide insights into the composition, stability, and functional potential of bacterial communities in slaughterhouse environments and their possible role in shaping pathogen and resistance gene dynamics along the food production chain.},
}

@article {pmid41713418,
year = {2026},
author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD},
title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.007},
pmid = {41713418},
issn = {1097-4172},
abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
}

@article {pmid41713270,
year = {2026},
author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D},
title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141525},
doi = {10.1016/j.jhazmat.2026.141525},
pmid = {41713270},
issn = {1873-3336},
abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.},
}

@article {pmid41713162,
year = {2026},
author = {Liu, X and Cai, H and Zhao, L and Ke, D and Xu, X and Li, J and Yu, J and Shen, Y and Zhu, L and Jin, Y and Zhang, M and Liu, S and Du, J and Zheng, J and Dong, R},
title = {Microplastic-associated gut microbial profile and antibiotic resistance in preschool children: a multicentre cross-sectional study in China.},
journal = {EBioMedicine},
volume = {125},
number = {},
pages = {106177},
doi = {10.1016/j.ebiom.2026.106177},
pmid = {41713162},
issn = {2352-3964},
abstract = {BACKGROUND: Microplastics (MPs) are ubiquitous in ecosystems and present in the human body, causing a worldwide environmental issue. However, the extent of human exposure to MPs remains largely unknown. Although mice exposed to MPs exhibit gut microbiota dysbiosis, the impact of MPs on the human intestinal microbiota remains unclear. Furthermore, MPs can carry and spread antibiotic resistance genes (ARGs). However, their potential influence on ARG abundance is underexplored.

METHODS: A multicentre cross-sectional study was conducted in Xiamen, Shanghai, and Nanjing in China from October 2022 to March 2023. A total of 335 couples of faecal samples were collected and analysed for MPs using Py-GC/MS and gut microbiota using 16S rRNA and metagenomic sequencing.

FINDINGS: Eight types of MPs were detected in 335 faecal samples, with a median concentration of 212.1 μg/g dw. MP exposure may be associated with the composition of the host gut microbiota. Microbial function analysis indicated the significant enrichment of 62 pathways primarily related to the metabolic pathways of macronutrients, vitamins, and bioactive substances. Total plastic concentration was significantly related to the relative abundance of species and ARGs, however this could not be attributed to specific plastic polymers after adjusting for covariates.

INTERPRETATION: This study provides baseline data on the gap in understanding of preschoolers' MP exposure, supporting the hypothesis that MP exposure might disrupt gut bacterial constitution and functions. This raises concerns regarding the potential adverse effects on the human gut when exposed to MPs, particularly drug resistance risks in younger populations.

FUNDING: Project of Shanghai Municipal Financial Professional foundation (Food Safety Risk Assessment) (grant number: RA-2023-10), National Natural Science Foundation of China (grant number: 2023YFF1104800), and Key Disciplines in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025) (grant number: GWVI-11.1-42).},
}

@article {pmid41713061,
year = {2026},
author = {Cokro, A and Albert Ng, TC and Hill, ED and Lee, C and Chandra Segeran, US and Arumugam, K and Williams, RBH and Wuertz, S},
title = {Microbial community biomarkers can forecast methane production in full-scale anaerobic digesters.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128828},
doi = {10.1016/j.jenvman.2026.128828},
pmid = {41713061},
issn = {1095-8630},
abstract = {Methane production from wastewater sludge via anaerobic digestion is a complex process and a disturbance in any one of the microbial stages can lead to eventual failure. Hence, it is desirable to detect disturbances as soon as possible. Although machine learning has been used to predict methane production from a variety of different substrates, there are no studies using metagenomic or -transcriptomic microbial community data as predictor variables. We used random forest analysis on a combination of physicochemical and microbial predictors to forecast methane production from three full-scale sludge digesters representing replicates of one another in a wastewater treatment plant in Singapore. Digesters were sampled for 25 weeks, and 42 physicochemical variables were measured along with shotgun metagenome and total RNA transcriptome sequencing. Models built using samples from a single digester yielded reactor-specific predictors, largely due to the limited sample size per reactor and the influence of rarer taxa. When data from the three digesters were combined, the best predictors included both substrate-related physicochemical parameters, such as chemical oxygen demand, and microbial taxa. Simulation using learning curves indicated that 150 to 200 samples instead of the 75 used would have yielded the most accurate methane prediction. The selection of many unidentified operational taxonomic units as microbial predictors suggests the existence of important yet unknown microorganisms in anaerobic digestion. The prediction model supports onsite digester surveillance by identifying digester-specific predictors through sufficient sampling, after which only those predictors need to be measured for subsequent monitoring.},
}

@article {pmid41712638,
year = {2026},
author = {Zhao, XD and Wang, YQ and Zhang, S and Li, JQ and Cai, YJ and Shu, X and Chen, Z and Zhang, SY},
title = {Spatially resolved denitrification coupled with methane and arsenite oxidation at the millimeter-scale straw-soil interface.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {8},
pages = {e2521285123},
doi = {10.1073/pnas.2521285123},
pmid = {41712638},
issn = {1091-6490},
support = {52270198//National Natural Science Foundation of China/ ; 42477116//National Natural Science Foundation of China/ ; JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Methane/metabolism ; Oxidation-Reduction ; *Denitrification ; *Arsenites/metabolism ; *Soil Microbiology ; *Soil/chemistry ; Nitrogen Fixation ; Nitrogen/metabolism ; },
abstract = {Straw return reshapes the biogeochemical processes in paddy soils by driving microbial transformation of key elements. Despite growing awareness of these individual processes, the integration of these processes under millimeter-scale spatiotemporal heterogeneity remains unclear. Combining high-resolution geochemical profiling with multiomics, we revealed that straw addition altered the depth-dependent dynamics of arsenic, carbon, and nitrogen, establishing a sophisticated three-layer microbial stratification. We identified 1) an 18 mm organic matter (OM)-rich layer extending from the straw layer, which serves as a methanogenic epicenter co-occurring with active nitrogen fixation microbes; 2) an overlying layer dominated by aerobic methane oxidation and denitrification microbes; and 3) a deeper substraw layer dominated by anaerobic arsenite oxidation and denitrification microbes. Significantly positively correlated abundances of transcribed mcrA with nifH genes and pmoA or aioA/arxA with denitrification genes were identified. Corroboratively, intensified co-occurrence patterns of mcrA with nifH, pmoA with denitrification, and aioA/arxA with denitrification genes were observed in the OM-rich, upper, and lower layers, respectively. Moreover, the co-occurred mcrA-nifH and aioA-nirS/arxA-narG genes in different metagenome-assembled genomes presented 80.6 to 260.8- and 1.55 to 6.85-fold greater transcriptional activity in the OM-rich and lower layers than in the other layers, respectively. Our results demonstrated that straw incorporation established a dynamic soil redox zone, restructuring millimeter-scale microbial networks and promoting potentially coupled denitrification with arsenite or methane oxidation, as well as methanogenesis with nitrogen fixation. These findings provide a mechanistic basis for optimizing subsurface straw placement and nitrate application to enhance nutrient cycling and mitigate environmental risks.},
}

*Methane/metabolism
Oxidation-Reduction
*Denitrification
*Arsenites/metabolism
*Soil Microbiology
*Soil/chemistry
Nitrogen Fixation
Nitrogen/metabolism

@article {pmid41712566,
year = {2026},
author = {Bedoya-Urrego, K and Peñuela-Martínez, AE and Alzate, JF},
title = {Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0332370},
pmid = {41712566},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Fermentation ; *Coffee/microbiology ; Phylogeny ; *Yeasts/genetics/classification ; Metagenome ; Biodiversity ; Genome, Fungal ; },
abstract = {Yeasts play a pivotal role in coffee fermentation, shaping microbial succession and contributing to the development of final flavor profiles. Despite their importance, yeast taxonomy in this context remains poorly resolved. Traditional classification methods often result in misidentifications due to the limited resolution of classical microbiological techniques and the rapidly evolving taxonomic framework driven by advances in phylogenomic. Moreover, the diversity of budding yeasts in coffee fermentations remains underexplored using high-resolution approaches such as metagenomics. To address this gap, we applied a shotgun metagenomic strategy and reconstructed metagenome-assembled genomes (MAGs) from multiple coffee fermentation samples and, using a robust phylogenomic framework based on 832 conserved single-copy genes. We confidently classified 22 yeast MAGs within the subphylum Saccharomycotina. These included well-known taxa such as Pichia kluyveri, Hanseniaspora spp., Torulaspora delbrueckii, and members of the Kurtzmaniella clade. Most MAGs were placed in strongly supported monophyletic groups (ultrafast bootstrap = 100), with short intra-clade branch lengths indicative of intraspecific variation. Pichia kluyveri emerged as the most abundant and widespread species, detected in all analyzed metagenomes, followed by Hanseniaspora spp. Our results underscore the power of high-resolution phylogenomic for classifying yeast MAGs and highlight the ecological importance of Pichia, Hanseniaspora, Torulaspora, and Kurtzmaniella in spontaneous coffee fermentations.},
}

*Metagenomics/methods
Fermentation
*Coffee/microbiology
Phylogeny
*Yeasts/genetics/classification
Metagenome
Biodiversity
Genome, Fungal

@article {pmid41712385,
year = {2026},
author = {Hong, J and Xue, W and Wang, T},
title = {Universal gene-level bimodality in natural microbial communities.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117013},
doi = {10.1016/j.celrep.2026.117013},
pmid = {41712385},
issn = {2211-1247},
abstract = {Bimodality-the coexistence of two peaks in trait distributions-is common in natural ecosystems. In microbiomes, bimodality of species abundances is known. However, whether this pattern applies to community functionality remains unclear. Here, we systematically investigate the abundance distributions of individual genes in different microbiomes, from human gut to ocean, revealing widespread gene-level bimodality. The bimodal genes are enriched in niche-specific pathways, suggesting their roles in ecological adaptation of the community. Based on their abundances, we develop a framework for microbiome functional typing, offering a gene-centric alternative to the taxonomy-based paradigm. Applied to the human gut, our approach identifies eleven genes exhibiting robust bimodality across western countries. These genes are associated with diseases such as liver cirrhosis. Machine learning models leveraging these genes are predictive of these diseases, underscoring their potential as clinically relevant biomarkers. Our work provides critical insights for microbiome functional architecture and has implications for microbiome-based diagnostics.},
}

@article {pmid41711928,
year = {2026},
author = {Farias, LABG and Viana Neto, OM and Lima Sobrinho, EP and de Melo, AGND and Pontes, IM and Gonçalves, BBS and Benevides, HP and Maia, SPO and Rodrigues, JLN and Perdigão Neto, LV},
title = {Streptococcus suis infection as an emerging zoonotic threat in Brazil: a One Health-based review.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {68},
number = {},
pages = {e19},
pmid = {41711928},
issn = {1678-9946},
mesh = {*Streptococcus suis/genetics/isolation & purification ; Brazil/epidemiology ; Animals ; *Streptococcal Infections/epidemiology/transmission/microbiology/diagnosis/veterinary ; Humans ; Swine ; One Health ; *Communicable Diseases, Emerging/epidemiology/microbiology ; *Bacterial Zoonoses/epidemiology/microbiology ; *Zoonoses/microbiology ; *Swine Diseases/microbiology/epidemiology ; },
abstract = {Streptococcus suis infection is an emerging zoonotic pathogen of growing concern in Brazil, particularly in the Northeast-a region lacking swine-focused surveillance. Although human contamination remains rare, they have been increasingly reported among individuals exposed to pigs or pork products, and most commonly present as central nervous system infections. Diagnostic challenges persist, especially related to culture-based methods, highlighting the need for advanced molecular tools like polymerase chain reaction and metagenomic Next-Generation Sequencing. Veterinary data reveal a high diversity of serotypes and concerning rates of antimicrobial resistance. These studies remain scarce in regions with reports of human infection. This review highlights the clinical, epidemiological, and microbiological aspects of S. suis in Brazil and underscores the importance of One Health approaches to enhance detection and prevention.},
}

*Streptococcus suis/genetics/isolation & purification
Brazil/epidemiology
Animals
*Streptococcal Infections/epidemiology/transmission/microbiology/diagnosis/veterinary
Humans
Swine
One Health
*Communicable Diseases, Emerging/epidemiology/microbiology
*Bacterial Zoonoses/epidemiology/microbiology
*Zoonoses/microbiology
*Swine Diseases/microbiology/epidemiology

@article {pmid41711914,
year = {2026},
author = {Demin, K and Onasenko, K and Beletskaya, A and Tsoy, A and Boyko, M and Kulikov, M and Kulikova, D and Prazdnova, E},
title = {Studying organosulfonate metabolism in southern Russia chernozem soil microbial community: ubiquity of the desulfonation pathways and possible mixotrophy in common soil heterotrophs.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {201},
pmid = {41711914},
issn = {1432-072X},
support = {SP-12-23-04//Priority 2030/ ; },
}

@article {pmid41711085,
year = {2026},
author = {Hart, LN and Errera, R and Godwin, C and Loftin, KA and Laughrey, ZR and Katona, LR and Johnson, EC and Cory, RM and Kiledal, EA and Den Uyl, P and Kharbush, JJ and Sherman, DH and Dick, GJ},
title = {Diverse Cyanopeptides Follow Distinct Temporal Succession Patterns in Freshwater Harmful Algal Blooms.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag026},
pmid = {41711085},
issn = {1751-7370},
abstract = {Toxic cyanobacterial harmful algal blooms (cyanoHABs) threaten freshwater resources globally and are intensifying with increasing eutrophication. Bloom toxicity is strongly influenced by intraspecific variation in the biosynthetic repertoires of toxic cyanobacteria, yet few studies examine the diversity of cyanobacterial cyanopeptides beyond hepatotoxic microcystins. To understand the dynamics and drivers of cyanopeptide diversity in cyanoHABs, we analyzed temporal patterns of cyanobacteria, metabolites, and their biosynthetic gene clusters (BGCs) in western Lake Erie using a seven-year time series (2016-2022) of metagenomic and metabolomic data. Our findings demonstrate that shifts from Microcystis to Dolichospermum occur later in the bloom season, coinciding with lower temperatures. Modules of co-varying BGCs (biosynthesis modules) from these genera were identified with hierarchical clustering, with uncharacterized BGCs among the most abundant. Biosynthesis modules rich in nonribosomal peptide synthetases (NRPS) peaked in early August, coinciding with elevated levels of inorganic nitrogen, warmer temperatures, and high Microcystis abundance. In contrast, modules rich in polyketide synthases (PKS) and ribosomally synthesized and post-translationally modified peptides (RiPPs) peaked following the Microcystis maximum in mid-August. Metabolomic analyses confirmed that metabolites followed shared seasonal patterns with their associated biosynthesis modules, forming three phases characterized by (1) microcystins, (2) anabaenopeptins and aeruginosins, and (3) aerucyclamides. These phases co-varied with bottom-up and top-down pressures, with later phases coinciding with increased microbially processed organic nitrogen and reduced detection of grazers. This study demonstrates consistent seasonal patterns of cyanobacterial metabolite succession and co-occurrence beyond microcystins, suggesting tradeoffs between biosynthetic resource demands and ecological controls.},
}

@article {pmid41711071,
year = {2026},
author = {Boeckel, C and Lisovski, S and Stoof-Leichsenring, KR and Weiß, JF and Liu, S and Harms, L and Herzschuh, U},
title = {DNA virus-host patterns in lake and marine environments over the last glacial cycle.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag025},
pmid = {41711071},
issn = {1751-7370},
abstract = {Viruses are integral to population dynamics, biogeochemical cycling, and host evolution, making them essential for ecosystem function. We explore long-term virus-host interactions mainly within microbial ecosystems in lake and marine environments across the late Pleistocene and Holocene. Sedimentary ancient DNA (sedaDNA) from five Siberian lakes and three Subarctic/Antarctic marine cores were analysed to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 357 161 reads (0.089% of total mapped reads), distributed across 2084 unique viral taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes from the Pleistocene to the Holocene, supporting sedaDNA as a tool to reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs documented in published literature, spanning bacterial, archaeal, and eukaryotic hosts, and assessed their associations based on co-occurrence correlations. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded after the Bering Strait opened, potentially due to absent viral infection, although database limitations prevent clear interpretation. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study demonstrates that sedaDNA time-series can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem-specific responses to environmental change.},
}

@article {pmid41711070,
year = {2026},
author = {Beauvais, M and Schatt, P and Soulié, T and Lambert, S and Montiel, L and Gaudin, M and Chaffron, S and Logares, R and Bouget, FY and Galand, PE},
title = {Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag029},
pmid = {41711070},
issn = {1751-7370},
abstract = {Marine microbial communities are fundamental to nutrient and biogeochemical cycling, with intricate networks of metabolic interdependencies influencing their structure and dynamics. Among these, vitamins B1 (thiamin) and B12 (cobalamin) play crucial roles as enzymatic cofactors in central metabolic pathways. Despite their importance, the temporal dynamics of vitamin production, bioavailability, and associated microbial interactions, remain poorly understood. Using a 7-year monthly metagenomic time series from the NW Mediterranean Sea (SOLA station), we found that vitamin B1/B12 auxotrophs (need for an exogenous vitamin source) were present throughout the year. Among B1 auxotrophs, those requiring the thiamin precursor HMP were the most prevalent, with peak abundances in summer. Distinct metagenome-assembled genome co-abundance patterns between B1 and B12 producers/auxotrophs across seasons suggested mutualistic relationships. Double B1/B12 vitamin complementarities were more common in summer, and single vitamin complementarity was dominant in winter. As previously shown for vitamin B12, which is limiting during winter, bioassays revealed variable availability of vitamin B1 in winter seawater despite the abundance of its producers, suggesting potential transfer of vitamin B1 among microorganisms. Finally, microcosm experiments showed that B1 and B12 amendments significantly influenced the composition of microbial communities, with temporal variations in their impact. In some cases, B12 and B1 amendments favored both vitamin auxotrophs and producers, highlighting complex interdependencies between B1 and B12 producers and consumers. Our findings highlight the complexity of B vitamin-mediated metabolic interactions that shape microbial community dynamics and underscore the need for long-term, high-resolution studies to better understand vitamin-driven ecological processes in marine systems.},
}

@article {pmid41710374,
year = {2026},
author = {He, L and Li, F},
title = {Clinicopathologic Features of Genitourinary Malakoplakia and Analytical Utility of the MetaPath Assay.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {582917},
pmid = {41710374},
issn = {1178-6973},
abstract = {PURPOSE: To describe the clinicopathological spectrum of genitourinary malakoplakia (MPL) and to evaluate the feasibility and clinical impact of metagenomic pathogen detection (MetaPath) performed on archival formalin-fixed paraffin-embedded (FFPE) tissue.

PATIENTS AND METHODS: Clinical imaging, histopathology, immunohistochemistry, special stains and MetaPath results were retrospectively analysed in five MPL cases diagnosed between January 2019 and August 2025.

RESULTS: The cohort comprised four men and one woman with a median age of 65.4 years. Four lesions arose in the prostate and one in the bladder. Histology showed chronic granulomatous inflammation with numerous eosinophilic histiocytes containing 5-10 µm targetoid Michaelis-Gutmann bodies. CD68 and CD163 were diffusely positive; PAS and iron stains highlighted the inclusions. MetaPath identified pathogens in 3/5 (60%) FFPE specimens (Escherichia coli in two, Pseudomonas aeruginosa in one). Antibiotic regimens were adjusted according to MetaPath results. After a median follow-up of 6 months (range 4-8) all patients remained symptom-free.

CONCLUSION: MPL is frequently misdiagnosed as malignancy. MetaPath can reliably detect pathogens in archival tissue and guide targeted antimicrobial therapy, representing a valuable adjunct to conventional culture.},
}

@article {pmid41710165,
year = {2026},
author = {Stevenson, Z and Schultz, DL and Chamberlain, M and Rico, K and Anbar, A and Dekas, AE and Swanner, ED},
title = {Lowering the Mo limit for nitrogen fixation by Mo-nitrogenase.},
journal = {Communications earth & environment},
volume = {7},
number = {1},
pages = {169},
pmid = {41710165},
issn = {2662-4435},
abstract = {Archean ocean marine primary productivity may have been limited by biologically available nitrogen. Due to low molybdenum abundances, early biological nitrogen fixation is thought to have relied on alternative nitrogenases that incorporate vanadium or iron instead of molybdenum. Here, we examine nitrogen fixation in a Cyanobacteria-dominated, ferruginous, low-sulfate, low-molybdenum lake, which replicates biological and chemical conditions relevant to early marine primary productivity. Nitrogen fixation occurs even when molybdenum is <1 nM, 100x less than the abundance in modern oceans. Molybdenum additions did not increase nitrogen fixation rates, indicating that diazotrophs were not molybdenum limited. Only the molybdenum-iron nitrogenase was detected in metagenomes and metatranscriptomes, indicating that the alternative nitrogenases were not required. We suggest that low sulfate (<1 μM) and/or efficient uptake mitigated molybdenum limitation. These results indicate that molybdenum bioavailability may be strongly controlled by sulfate and that alternative nitrogenases are not essential for nitrogen fixation at low molybdenum.},
}

@article {pmid41710035,
year = {2026},
author = {John, J and Ortiz, M and Ramond, P and Campbell, BJ},
title = {Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag021},
pmid = {41710035},
issn = {2730-6151},
abstract = {Functional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbations.},
}

@article {pmid41709890,
year = {2026},
author = {Dai, L and Zhan, W and Huang, X and Lyu, L and Jiang, S and Zhou, P},
title = {Refractory multiple brain abscesses caused by Prevotella loescheii and Porphyromonas gingivalis: successful endoscopic lavage and drainage: a case report and review of the literature.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1736006},
pmid = {41709890},
issn = {2296-858X},
abstract = {BACKGROUND: Brain abscesses represent life-threatening conditions, with management complexities significantly heightened in cases involving multiple lesions that are refractory to standard empirical therapies. Prevotella loescheii and Porphyromonas gingivalis, anaerobic bacteria typically residing within the oral flora, are infrequent yet formidable pathogens responsible for intracranial abscess formation. The fastidious nature of these microorganisms often results in delayed diagnosis and initiation of targeted treatment.

CASE PRESENTATION: A 25-years-old male presented with a 1-month history of cough, sputum production, and persistent high-grade fever reaching 41 °C. Initially diagnosed with a brain abscess at a local hospital, he received empirical treatment with ceftriaxone, acyclovir, and mannitol, which failed to yield clinical improvement. His condition subsequently deteriorated, characterized by disturbances in consciousness and dysarthria. The antimicrobial regimen was escalated to include vancomycin and meropenem. Despite these efforts, the patient's neurological status continued to decline, with imaging studies revealing the development of multiple new intracranial abscesses and diffuse intracranial hypertension. Surgical intervention was undertaken, involving abscess excision and decompressive craniectomy. Postoperative imaging 1 week later showed further abscess expansion and the onset of right-sided hemiplegia. Upon admission to our institution, metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid identified the presence of Prevotella loescheii and Porphyromonas gingivalis. The antimicrobial regimen consisting of vancomycin and meropenem was maintained, and the patient underwent endoscopic intracranial abscess lavage with burr hole external drainage. This integrated approach led to significant radiographic resolution of the abscesses and a gradual improvement in the patient's level of consciousness. The refractory infection was traced back to an oropharyngeal source.

CONCLUSION: This case highlights the critical diagnostic value of mNGS in detecting fastidious oral anaerobic pathogens in culture-negative refractory brain abscesses. It illustrates that a combination of targeted antibiotic therapy and minimally invasive surgical intervention-specifically, endoscopic lavage and drainage-can be highly effective in managing complex, multi-loculated abscesses caused by Prevotella loescheii and Porphyromonas gingivalis. Maintaining a high index of suspicion for an odontogenic or oropharyngeal origin is crucial in the diagnostic evaluation of such infections.},
}

@article {pmid41514270,
year = {2026},
author = {González-Rovira, M and Sainz-Bueno, JA and García-Díaz, L and Martínez-Pancorbo, C and Sánchez, J and Gutiérrez, G and Magoutas, K and Mesías-Pérez, A and Mellado, E and Payne, M and Sousa, C and Moreno, ML},
title = {Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {273},
pmid = {41514270},
issn = {1479-5876},
support = {PID2024-157768OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; SUBN/2019/005//Federación de Asociaciones de Celíacos de España (FACE)/ ; US-15332/I+D+I//FEDER ANDALUCIA/ ; },
abstract = {BACKGROUND: The evidence of a low-biomass microbial community in the amniotic fluid (AF) is challenging the traditional concept of a sterile womb. To clarify microbial presence and host responses, a comprehensive, multi-methodological approach is required.

METHODS: We designed an optimized culturing strategy that maximized microorganism recovery by implementing differential centrifugation and concentration of AF samples, followed by plating onto four distinct selective media types and incubation under both stringent aerobic (up to two weeks) and prolonged anaerobic (up to four weeks) conditions, including an initial pre-enrichment step in Brain Heart Infusion (BHI) broth for low-abundance organisms. These results were combined with PacBio 16S rRNA gene sequencing, Illumina shotgun metagenomics, and antimicrobial peptides (AMP) detection. Using this approach, we characterized microbial presence in 154 AF samples across gestational stages. Data normality was assessed with the Shapiro-Wilk test, guiding the selection of both parametric and non-parametric tests, and a p-value of < 0.05 was considered statistically significant.

RESULTS: We detected culturable microorganisms in 33.1% of samples, with a higher proportion in elective caesarean Sect. (55.0%) compared to amniocentesis (29.5%), suggesting increased microbial load toward term. We applied stringent contamination controls, and repeatedly recovered viable microorganisms Bacillus, Cutibacterium, Micrococcus, and Staphylococcus, with Cutibacterium acnes and Staphylococcus epidermidis common. Both sequencing methods revealed a low-biomass, low-diversity microbial community with high inter-individual variability. Notably, striking microbial discordance in diamniotic twin pregnancies, challenged intrauterine homogeneity. Higher Human Beta Defensin (HBD) -1 levels correlated with absence of culturable bacteria or microbial DNA, while levels of HBD-1, HBD-3, and LL-37 were reduced in Staphylococcus-positive samples, suggesting a dynamic interplay between specific bacteria and host defences.

CONCLUSIONS: Our findings indicate that viable bacteria and/or DNA can transiently access the prenatal environment microbial balance. We propose a novel perspective of a potential regulatory axis between microorganisms and AMP.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07601-0.},
}

@article {pmid41709323,
year = {2026},
author = {Yin, S and Xiao, Z and Yu, Z and Zhou, C and Jian, J and Xiao, Y and Yang, H},
title = {Iterative enrichment cultivation and multiomic analysis reveal potential endophytic bacteria affecting the sinomenine synthesis in Sinomenium acutum.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-026-02965-4},
pmid = {41709323},
issn = {1475-2859},
abstract = {Endophytes play important roles in plant metabolite synthesis, and certain strains were capable of producing bioactive compounds identical to those of their hosts. However, it remains unknown whether culturable endophytes of S. acutum can synthesize intermediate metabolites for the plant principal bioactive compound-sinomenine (SIN) or the compound itself. In this study, we investigated the successions of the culturable bacterial community and the alkaloid profiles within S. acutum endophytes across ten iterative enrichment cultivations using Czapek-Dox and Gause's No. 1 chemically defined media. The results demonstrated significant alterations in the composition and structure of the endophytic consortium and metabolites of the endophytic consortium during iterative cultivation. Priestia aryabhattai dominated the community in the first generation, whereas Microbacterium paraoxydans and Bacillus velezensis became dominant by the tenth generation. SIN was detected at the first and the fifth generation, with declining concentrations, and was absent at the tenth generation. Correlation network analysis revealed a strong positive correlation between the relative abundance of P. aryabhattai and the SIN content. Furthermore, a specific strain, L15, identified as P. aryabhattai, was isolated from the iterative culture. UPLC-MS/MS analysis of P. aryabhattai L15 metabolites confirmed the presence of SIN, alongside other alkaloids including cyclanoline, N-methylhigenamine-7-O-glucopyranoside, and isoquinoline. Further metagenomic analysis also indicated that the relative abundance of P. aryabhattai was significantly (p < 0.05) positively correlated with the SIN content in plant tissues. This study systematically elucidated the role of endophytic bacteria and provides potential strains for the synthesis of bioactive compounds and pharmaceutical research.},
}

@article {pmid41709267,
year = {2026},
author = {Baquer, F and Grillon, A},
title = {Interaction between tick and host microbiotas: a four-step waltz.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07308-1},
pmid = {41709267},
issn = {1756-3305},
abstract = {Tick-borne diseases represent a growing public health concern worldwide, yet the microbial factors that govern pathogen transmission remain incompletely understood. Over the past decade, high-throughput metagenomics and functional studies have revealed that two distinct microbial communities-the vertebrate host's skin microbiota and the tick's own microbiome-act synergistically as key modulators of pathogen acquisition, persistence within the vector, and successful transmission to the vertebrate host. At the feeding site, the skin microbiota orchestrates local cutaneous immunity, influences inflammatory responses, and can either hinder or inadvertently facilitate dermal establishment of tick-borne pathogens such as Borrelia burgdorferi sensu lato (s.l.), Anaplasma phagocytophilum, Rickettsia species, Babesia spp., and tick-borne encephalitis virus. Tick feeding itself induces rapid and sometimes long-lasting dysbiosis of the skin microbial community, creating temporal windows of vulnerability for pathogen invasion. Concurrently, within the tick vector, a core set of endosymbiotic bacteria, including Rickettsia buchneri, Midichloria mitochondrii, Coxiella-like, and Francisella-like endosymbionts, engage in complex mutualistic, competitive, and facilitative interactions. These symbionts regulate vector competence through nutrient provisioning (especially B-vitamins), direct competition for niche space, and immune priming or suppression of the tick's innate immune system. Such interactions ultimately determine the maintenance, abundance, and transmissibility of tick-borne pathogens. By integrating these dual host-vector microbiome perspectives in a comprehensive review, we highlight emerging mechanistic insights into transmission ecology and biologically grounded targets for the prevention and control of tick-borne diseases, including anti-microbiota vaccines and paratransgenic and microbiome-based approaches.},
}

@article {pmid41709052,
year = {2026},
author = {Idris, H and Hairi, HH and Ahmad, A and Danish-Daniel, M and Zin, NM and Sanderson, RA and Raja Yahya, MFZ and Majhool, AA and Hassan, MY and Azman, MAZ},
title = {Revealing actinobacterial diversity inhabiting Malaysian Beach Ridges Interspersed with Swales (BRIS) soil : insights from culture-dependent and metagenomic approaches.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41709052},
issn = {1618-1905},
}

@article {pmid41708925,
year = {2026},
author = {Wawina-Bokalanga, T and Makangara-Cigolo, JC and Ola-Mpumbe, R and Lokilo, E and Mwakisenda-Tshakotsho, F and Delphine, M and Kahindo, I and Tshonaka-Nkololo, A and Vakaniaki, EH and Loman, N and Houben, S and Lumembe-Numbi, R and Kinganda-Lusamaki, E and Ponga-Museme, A and Mukota-Nungu, Y and Kumar, A and Meris, M and Wilkinson, S and Colquhoun, R and Kenye, KM and Akil-Bandali, P and Amuri-Aziza, A and Martinez, GS and Kelvin, DJ and Dijkman, R and Hensley, LE and Kasita, C and Kafua-Wemba, F and Mwamba, D and Subissi, L and Hoff, NA and Peeters, M and Rimoin, AW and Mokili, JL and Lunguya-Metila, O and Nkwembe, E and Rambaut, A and Liesenborghs, L and Low, N and Kindrachuk, J and Vercauteren, K and Edwards, R and Kelly, JN and Mbala-Kingebeni, P and Ahuka-Mundeke, S and Mumba, D and Muyembe-Tamfum, JJ},
title = {Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41708925},
issn = {1546-170X},
abstract = {In late 2024, an outbreak of over 400 cases of undiagnosed febrile illness, predominantly presenting as fever and cough, was reported in Panzi Health Zone, southwestern Democratic Republic of the Congo. Here we conducted an epidemiological and laboratory investigation to determine the etiology of the outbreak. Clinical data and specimens were prospectively collected from 108 individuals, of whom 59/108 (54.6%) were female. Children aged <5 years were the most affected (47/108, 43.5%); 14/32 (43.7%) were malnourished. Oro/nasopharyngeal swabs from 96/108 individuals were PCR tested; 26 blood samples were sequenced. Plasmodium falciparum was detected in 56/108 (51.8%) individuals. Co-infections were also detected, with influenza A(H1N1)pdm09 virus in 16/56 (28.6%) and severe acute respiratory syndrome coronavirus 2 in 10/56 (17.9%) individuals. No novel pathogens were detected via metagenomics. Our findings suggest that the outbreak was primarily associated with a surge in malaria cases, with concurrent viral respiratory infections. Increasing decentralized laboratory capacity and strengthening broader health systems remain crucial for faster outbreak detection and investigation.},
}

@article {pmid41708882,
year = {2026},
author = {K-Jánosi, K and Sztojka, A and Kis, IE and Biksi, I and Bakos, Z and Kaszab, E and Mag, T and Albert, E},
title = {Characterisation of Salmonella Typhimurium from a fatal equine nosocomial outbreak and retrospective analysis of equine clinic salmonellosis cases (2010-2025).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40617-0},
pmid = {41708882},
issn = {2045-2322},
}

@article {pmid41708851,
year = {2026},
author = {Appler, KE and Lingford, JP and Gong, X and Panagiotou, K and Leão, P and Langwig, MV and Greening, C and Ettema, TJG and De Anda, V and Baker, BJ},
title = {Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41708851},
issn = {1476-4687},
abstract = {Asgard archaea were pivotal in the origin of complex cellular life[1]. Heimdallarchaeia (a class within the phylum Asgardarchaeota) are inferred to be the closest relatives of eukaryotes. Limited sampling of these archaea constrains our understanding of their ecology and evolution[2,3], including their role in eukaryogenesis. Here we use massive DNA sequencing of marine sediments to obtain 404 Asgardarchaeota metagenome-assembled genomes, including 136 new Heimdallarchaeia and several novel lineages. Analyses of their global distribution revealed they are widespread in marine environments, and many are enriched in variably oxygenated coastal sediments. Detailed metabolic reconstructions and structural predictions suggest that Heimdallarchaeia form metabolic guilds that are distinct from other Asgardarchaeota. These archaea encode hallmark proteins of an aerobic lifestyle, including electron transport chain complex (IV), haem biosynthesis and reactive oxygen species detoxification. Heimdallarchaeia also encode novel clades of respiratory membrane-bound hydrogenases with additional Complex I-like subunits, which potentially increase proton-motive force generation and ATP synthesis. Thus, we propose an updated Heimdallarchaeia-centric model of eukaryogenesis in which hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor. This expanded catalogue of Asgard archaeal genomic diversity suggests that bioenergetic factors influenced eukaryogenesis and constitutes a valuable resource for investigations into the origins and evolution of cellular complexity.},
}

@article {pmid41708335,
year = {2026},
author = {Hkimi, C and Yaiche, H and Kamoun, S and Ben Aissa-Haj, J and Boujemaa, M and Abdelhak, S and Ghedira, K and Hamdi, Y},
title = {OMICs data from Tunisian population: challenges and opportunities in the era of precision medicine.},
journal = {Personalized medicine},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/17410541.2026.2632096},
pmid = {41708335},
issn = {1744-828X},
abstract = {OBJECTIVE: The transition to precision medicine (PM) is revolutionizing healthcare by enabling diagnostics and treatments tailored to individual molecular and genetic profiles, with omics sciences at its core. In Tunisia, growing interest is seen through initiatives such as Personalized Medicine in North Africa (PerMediNA).

METHODS: This study assesses Tunisia's readiness for PM by mapping publicly available omics datasets and related publications using Tunisian human data. A structured search across PubMed and major repositories covered studies published between 2010 and 2023 involving high-throughput technologies.

RESULTS: A total of 11 omics datasets were found, mainly genomic, alongside 104 publications, of which 96 focused on genomics. Whole exome sequencing (n = 46) and targeted gene panels (n = 37) were the most used approaches. Only six proteomics, one transcriptomics, and one metagenomics studies were identified; no epigenomics or metabolomics datasets were found. Research centered mainly on cancers, including breast, colorectal, and leukemia. While Tunisia shows progress in genomics, major gaps exist in other omics domains.

CONCLUSIONS: Advancing PM in Tunisia requires establishing a national omics data repository with ethical governance, promoting North - South collaborations to build capacity in non-genomic omics fields, and fostering public - private partnerships to strengthen infrastructure, data sharing, and sustainable research development.},
}

@article {pmid41708296,
year = {2026},
author = {Huang, J and Zhang, J and Liang, H and Fang, P and Tang, A and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Lin, L and Li, X and Li, B},
title = {Antibiotics or Heavy Metals in Livestock Wastewater: Which One Is the Main Driver for the Development and Spread of Antibiotic Resistance under Coexposure?.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06042},
pmid = {41708296},
issn = {1520-5851},
abstract = {Antibiotics and heavy metals are widely used in livestock farming to promote animal health and growth, leading to their frequent co-occurrence as contaminants in livestock wastewater. However, their relative contributions to shaping the antibiotic resistome in treatment systems remain unclear. In this study, we simulated an aerobic activated sludge process treating livestock wastewater containing enrofloxacin and heavy metals (Cu[2+] and Zn[2+]) to evaluate the development of antibiotic resistance using metagenomic and metatranscriptomic approaches. We observed a diverse and transcriptionally active resistome with over half of the detected antibiotic resistance genes (ARGs) showing expression. ARG profiles under coexposure to enrofloxacin and heavy metals more closely resembled those under heavy metal exposure alone than those under enrofloxacin exposure alone. Zn[2+] exposure resulted in the highest absolute ARG abundance, nearly double that of the control group. Both enrofloxacin and heavy metals significantly altered the abundance and phylogenetic composition of the antibiotic-resistant bacteria (ARB). The exposure to Zn[2+] enhanced the relative abundance and expression level of both metal resistance genes (MRGs)-carrying ARB and the ARGs-carrying plasmids. Phylogenetic analysis of ARG flanking sequences revealed high homology across various genetic contexts. Among mobile genetic elements, plasmids had a greater influence on ARG profiles than did phages or integrative and conjugative elements (ICEs). Transcriptional profiles of microbial physiological adaptations suggested that modulation of cell membrane permeability, promotion of conjugative transfer, and formation of biofilm might play roles in enhancing antibiotic resistance. These findings suggest at environmentally relevant concentrations, heavy metals such as Zn[2+] may present a stronger selective pressure than enrofloxacin for the propagation of antibiotic resistance in aerobic activated sludge process treating livestock wastewater.},
}

@article {pmid41708187,
year = {2026},
author = {Fang, M and He, J and Zhou, S and Hong, P and Ke, L and Wu, H and Shu, Y},
title = {Pleurotus ostreatus polysaccharides improve microcystin-LR-induced intestinal damage in tadpoles by regulating the interaction between microbiota and intestine.},
journal = {Harmful algae},
volume = {153},
number = {},
pages = {103056},
doi = {10.1016/j.hal.2026.103056},
pmid = {41708187},
issn = {1878-1470},
mesh = {Animals ; *Intestines/drug effects/microbiology ; *Microcystins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Pleurotus/chemistry ; *Polysaccharides/pharmacology ; Larva/drug effects/microbiology ; *Ranidae ; Marine Toxins ; Oxidative Stress/drug effects ; },
abstract = {Exposure to microcystins (MCs) can cause severe intestinal damage. This study aimed to assess the efficacy of Pleurotus ostreatus polysaccharide in alleviating intestinal damage induced by microcystin-leucine-arginine (MC-LR) in tadpoles. Over a 30-day period, tadpoles (Pelophylax nigromaculatus) received daily exposures to MC-LR and were provided with diets either supplemented with or devoid of P. ostreatus polysaccharide. Results revealed that feeding P. ostreatus polysaccharide conferred protection against MC-LR-induced intestinal damage by mitigating barrier damage, lowering intestinal permeability, and reducing the tissue burden of MC-LR. The LPS/TLR4 pathway response was attenuated, reducing inflammation, and oxidative stress-mediated apoptosis response was also diminished. Gram-negative bacteria (e.g., Bacteroides) in the intestine show a positive correlation with LPS content and the transcription of key genes in the LPS/TLR4 pathway. Metagenomic and metabolite analysis of intestinal contents revealed increased abundance of the alanine-glyoxylate aminotransferase gene (agxt)-the key enzyme converting glyoxylic acid to glycine-and elevated glycine content in the MC-LR-exposed group fed polysaccharide. Results from the corresponding fecal microbiota transplantation experiment aligned with the trends observed in the exposure experiment. Therefore, polysaccharide alleviates MC-LR-induced intestinal damage by enhancing intestinal microbiota-mediated glycine synthesis, supplying raw materials for intestinal GSH production, reducing oxidative stress levels, and simultaneously dampening the LPS/TLR4 pathway response. Moreover, feeding polysaccharides might also regulate the intestine's defense against pathogens after MC-LR exposure by enhancing lysozyme activity. There is no evidence of intestinal damage in the P. ostreatus exopolysaccharide group. This study highlights for the first time the role of P. ostreatus polysaccharides in mitigating MC-LR-induced intestinal tissue damage, potentially offering novel insights for their application in aquaculture.},
}

Animals
*Intestines/drug effects/microbiology
*Microcystins/toxicity
*Gastrointestinal Microbiome/drug effects
*Pleurotus/chemistry
*Polysaccharides/pharmacology
Larva/drug effects/microbiology
*Ranidae
Marine Toxins
Oxidative Stress/drug effects

@article {pmid41708005,
year = {2026},
author = {Lin, CC and Uno, H and Yamada, C and Terada, T and Lu, TJ and Fushinobu, S},
title = {Structural insights into glycoside hydrolase family 1 β-glucosidase: Selective oligosaccharide hydrolysis, synthesis, and product profiling.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111293},
doi = {10.1016/j.jbc.2026.111293},
pmid = {41708005},
issn = {1083-351X},
abstract = {β-Glucosidases are essential enzymes in plant cell wall metabolism and have diverse biotechnological applications, including cellulose degradation and prebiotic oligosaccharide synthesis. Td2F2, a glycoside hydrolase family 1 (GH1) β-glucosidase derived from a compost metagenome, exhibits a unique preference for sophorose. However, the molecular basis of this specificity as remains unclear. In this study, we determined high-resolution crystal structures of Td2F2 in complex with sophorose (1.64 Å) and laminaribiose (1.16 Å) using sodium malonate as a cryoprotectant. Structural analysis, complemented by molecular dynamics simulations, revealed a distinct subsite +1', where Asn223, Thr225, Glu296, and Arg325 form hydrogen bonds with the reducing-end glucose of sophorose, stabilizing an alternative, non-productive binding mode adjacent to the catalytic subsites. Site-directed mutagenesis confirmed that residues in subsite +1' residues are critical for substrate specificity. Guided by structural insights, we designed T225N and E296D mutants, which exhibited enhanced hydrolytic activity toward sophorose. To further investigate the transglycosylation potential of Td2F2, we characterized its dynamic product profile, ranging from disaccharides to tetrasaccharides, using porous graphitic carbon liquid chromatography-orbitrap tandem mass spectrometry. When p-nitrophenyl β-D-glucopyranoside and glucose were used as substrates, Td2F2 preferentially formed β-1→2 and β-1→3 linkages. These findings provide structural evidence that the subsite +1' is a "waiting position" in the GH1 β-glucosidase, offering novel insights into its role in hydrolysis and transglycosylation selectivity. This structural and functional framework paves the way for future GH1 enzyme engineering and expanded biotechnological applications.},
}

@article {pmid41707923,
year = {2026},
author = {do Nascimento, AC and de Albuquerque, TMR and de Oliveira, DG and de Oliveira, AP and da Costa, PCT and de Sales, LCS and da Silva, JYP and Lins, JDS and E Silva, AL and da Silva, EF and do Nascimento, YM and Tavares, JF and Lima, MDS and Bezerra, TKA and de Oliveira, MEG and El-Bacha, T and Alves, JLB and de Souza, EL},
title = {Integrated metagenomic and metabolomic profiling in an in vitro colonic fermentation study to assess the impacts of conventional, unconventional, and whole edible beet (Beta vulgaris L.) parts on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110316},
doi = {10.1016/j.jnutbio.2026.110316},
pmid = {41707923},
issn = {1873-4847},
abstract = {Beet (Beta vulgaris L.) has been widely studied as a functional food, particularly for its bioactive compounds. This study evaluated the physicochemical characteristics, nutritional composition, antioxidant capacity, and the impacts of freeze-dried beet root (FDBR), freeze-dried beet stems and leaves (FDBSL), and freeze-dried whole beet (FDWB) on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals. FDBR, FDBSL, and FDWB had high nutritional value. FDWB had the highest protein content (10.6 g/100 g), while FDBSL had the highest total dietary fiber content (46.6 g/100 g). Twenty-eight phenolic compounds were identified, and the antioxidant capacity reached up to 60.6 µmol Trolox/g in FDBR. 16S rRNA amplicon sequencing analysis demonstrated that colonic fermentation of FDBR, FDBSL, and FDWB with fecal inoculum from hypertensive individuals decreased the Firmicutes/Bacteroidetes ratio, decreased or maintained the bacterial diversity, increased the relative abundance of Bifidobacteriaceae, Lactobacillaceae, and Enterobacteriaceae, and decreased Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae. Colonic fermentation of FDBR mainly increased the abundance of Bifidobacterium (1.18%-7.63%), while FDBSL increased the abundance of Phocaeicola. FDBR, FDBSL, and FDWB decreased the pH values (6.74-5.09) and altered the metabolic profile during colonic fermentation by consuming sugar and producing several metabolites associated with health-promoting properties, while maintaining antioxidant capacity. FDBR, FDBSL, and FDWB may be circular resources with beneficial effects on the composition and metabolic responses of the intestinal microbiota in hypertensive individuals and could be exploited as dietary adjuvant strategies in the management of arterial hypertension.},
}

@article {pmid41707775,
year = {2026},
author = {Yu, S and Jin, Y and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J},
title = {Capacitive bimetallic redox cycles and ligand-to-metal charge transfer to Boost denitrification with Ni[II]/Fe[II]-Gallic acid phenolic networks.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134237},
doi = {10.1016/j.biortech.2026.134237},
pmid = {41707775},
issn = {1873-2976},
abstract = {Biological denitrification is limited by slow nitrate (NO3[-]) reduction due to low electron transfer efficiency, unsatisfactory community functional efficiency and insufficient metabolic activity of microbial communities. To overcome these challenges, Ni[2+] and Fe[2+] were incorporated with gallic acid (GA) to form bimetallic polyphenol networks (NiFeGA BPNs) with low-cost and high-biocompatibility. NiFeGA BPNs exhibited capacitive Ni(II)/Fe(II) redox cycles and excellent ligand-to-metal charge transfer capabilities to enable complete degradation of 200 mg/L NO3[-] within 8 h. All these improvements could be ascribed to that NiFeGA BPNs significantly improved electron transfer efficiency and stimulated microbial metabolic activity, which were proved by extracellular polymeric substances electrochemical analysis and electron transport chain inhibitors experiments. More importantly, metagenomic sequencing analysis confirmed that NiFeGA BPNs improved community structure by directionally enriching Pseudomonas. Consequently, NiFeGA BPNs significantly improving denitrification, which provides both theoretical guidance and technical frameworks for the continuous and efficient treatment of nitrate in wastewater.},
}

@article {pmid41707528,
year = {2026},
author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y},
title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119865},
doi = {10.1016/j.ecoenv.2026.119865},
pmid = {41707528},
issn = {1090-2414},
abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.},
}

@article {pmid41707490,
year = {2026},
author = {Jian, Z and Zhao, R and Zi, X and He, S and He, X and Ye, Y and Wang, K and Ge, C and Jia, J and Hu, Y and Dou, T},
title = {Sustainable antibiotic reduction in poultry production with Pulsatilla saponins and herbal supplementation.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106562},
doi = {10.1016/j.psj.2026.106562},
pmid = {41707490},
issn = {1525-3171},
abstract = {The prolonged use of antibiotics in poultry production promotes the accumulation and spread of antibiotic resistance genes (ARG), raising concerns for animal health and public safety. Developing effective antibiotic alternatives that support performance while limiting resistance risk is therefore a priority. Using broiler chickens as a model, this study evaluated the effects of Pulsatilla saponins, alone or combined with a compound herbal formulation, on growth performance, immune responses, cecal microbiota, and the intestinal resistome, with an antibiotic-treated group as reference. Growth and immune parameters were integrated with shotgun metagenomic sequencing to characterize microbial and ARG responses to dietary interventions. Compared with antibiotic supplementation, the combination of 0.5% herbal medicine and 0.6% Pulsatilla saponins (ZBZ) combination significantly enhanced immune traits, including spleen index and serum IgA and IgM levels, while increasing cecal microbial diversity and reshaping community composition. Metagenomic analyses showed that antibiotic treatment enriched efflux pump and target modification associated ARG, indicative of a multidrug resistance profile. In contrast, ZBZ markedly reduced the abundance and diversity of multidrug resistance-related ARG. Notably, ZBZ supplementation enriched short-chain fatty acid-producing taxa that were negatively correlated with multiple ARG classes, suggesting that improvements in the intestinal metabolic environment and colonization resistance constrained the expansion of resistant bacteria. Overall, the combined use of Pulsatilla saponins and a compound herbal formulation improved growth and immune performance while reducing intestinal ARG burden through coordinated modulation of the cecal microbiota-resistome axis, providing a sustainable nutritional strategy for antibiotic-reduced poultry production.},
}

@article {pmid41707423,
year = {2026},
author = {Francés, Á and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M},
title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.},
journal = {International journal of food microbiology},
volume = {452},
number = {},
pages = {111667},
doi = {10.1016/j.ijfoodmicro.2026.111667},
pmid = {41707423},
issn = {1879-3460},
abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.},
}

@article {pmid41707391,
year = {2026},
author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K},
title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110926},
doi = {10.1016/j.vetmic.2026.110926},
pmid = {41707391},
issn = {1873-2542},
abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.},
}

@article {pmid41707316,
year = {2026},
author = {Yang, J and Meng, X and Zhang, H and Sun, W and Yang, L and Li, S},
title = {Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water-sediment interface.},
journal = {Environmental research},
volume = {296},
number = {},
pages = {124055},
doi = {10.1016/j.envres.2026.124055},
pmid = {41707316},
issn = {1096-0953},
abstract = {Riverine ecosystems are major conduits and repositories for microplastics, heavy metals and antibiotics yet how these co-occurring stressors jointly shape resistance and virulence risks across water and sediments remains unclear. Here we combined shotgun metagenomics with pollutant profiling along a representative rural-to-urban gradient during the dry season to resolve the distribution, mobility and drivers of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), virulence factors (VFs) and mobile genetic elements (MGEs) in paired surface waters and surficial sediments. Bacterial communities were dominated by Pseudomonadota and Actinomycetota while fungal communities were dominated by Ascomycota and Uroviricota respectively with stronger land-use effects observed in water than in sediments. Across all samples we detected 36 ARG classes and 1589 subtypes where multidrug and efflux or target alteration mechanisms predominated. Furthermore ARG richness, abundance and diversity increased from rural to urban reaches in both media. MGEs were dominated by transposases where ARG-MGE co-localization on 1474 contigs revealed dense transposase-centered networks in urban sediments that linked multidrug, peptide, glycopeptide and tetracycline resistance. Crucially we identified contigs co-harboring ARGs, MRGs, and VFs as multi-trait risk gene carriers. Urban reaches hosted diverse carrier lineages whereas rural reaches were dominated by the high abundance of specific carriers. SourceTracker and partial least squares path modeling together indicated that rural sediments are the principal upstream sources of microbes and risk genes while MGEs in urban sediments translate multi-pollutant stress into enlarged and more mobile risk gene pools. These findings highlight the need to jointly manage agricultural inputs and urban sediments under multi-stressor conditions.},
}

@article {pmid41707285,
year = {2026},
author = {Du, Z and Li, Z and Chen, X and Liu, M and Feng, L and Li, Q and Chen, Z and Chen, Q},
title = {Laboratory-scale simulation study on the bioremediation of marine oil pollution by phosphate-solubilizing bacteria Bacillus subtilis PSB-1.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119422},
doi = {10.1016/j.marpolbul.2026.119422},
pmid = {41707285},
issn = {1879-3363},
abstract = {Phosphate-solubilizing bacteria (PSB) are well-known for their ability to convert nonbioavailable phosphates into bioavailable forms, however, research on PSB that possess both phosphate solubilization and crude oil degradation capabilities in marine environments has not yet been explored, and the role of these bacteria in microbial remediation of petroleum contamination in seawater needs be investigated. In this study, laboratory simulated marine oil spill bioremediation experiment was carried out to explore the role of PSB with crude oil degradation capabilities (A strain of PSB-1 used in this study) in petroleum hydrocarbon degradation by indigenous microorganisms in marine environment. It was found that PSB-1 significantly enhanced crude oil removal, with a degradation efficiency of 60% achieved after 30 days at a crude oil concentration of 1 g/L, Concurrently, the concentration of soluble phosphate in seawater increased to 47.36 mg/L, reflecting a 170% increase compared to the control. Metagenomic analysis further indicated that the phosphate-solubilizing activity of PSB-1 not only augmented phosphate availability but also stimulated the growth and succession of indigenous hydrocarbon-degrading microorganisms, thereby altering the microbial community structure and improving overall degradation capacity. These findings highlight the ecological significance of PSB-1 in facilitating crude oil biodegradation in marine environments and offer novel insights into bioremediation strategies for crude oil-contaminated seawater.},
}

@article {pmid41707175,
year = {2026},
author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W},
title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0279},
pmid = {41707175},
issn = {1480-3275},
abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of P. rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during P. rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.},
}

@article {pmid41706260,
year = {2026},
author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T},
title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {},
number = {},
pages = {},
pmid = {41706260},
issn = {1436-3305},
support = {Research Project Grant//Kawasaki Medical School/ ; },
}

@article {pmid41705859,
year = {2026},
author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM},
title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0134625},
doi = {10.1128/mra.01346-25},
pmid = {41705859},
issn = {2576-098X},
abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.},
}

@article {pmid41705858,
year = {2026},
author = {Teixeira Martins, C and Gombert, AK and Venturini, AM},
title = {Lactobacillus and Limosilactobacillus MAGs from alcoholic fermentation in sugarcane biorefineries.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mra.00705-25},
pmid = {41705858},
issn = {2576-098X},
abstract = {We recovered and characterized four bacterial MAGs from two Brazilian sugarcane biorefineries, with the aim of investigating the microbial environment during fuel ethanol production. MAGs belonged to Lactobacillus amylovorus and Limosilactobacillus fermentum, both known lactic acid bacterial contaminants. Genomic analyses revealed key functional traits but no resistance or virulence genes.},
}

@article {pmid41705822,
year = {2026},
author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K},
title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0242225},
doi = {10.1128/aem.02422-25},
pmid = {41705822},
issn = {1098-5336},
abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.},
}

@article {pmid41705811,
year = {2026},
author = {Paietta, EN and Kraberger, S and Gordon, M and Ehmke, E and Yoder, AD and Varsani, A},
title = {Metagenome-assembled genomes of anelloviruses in crowned lemur and aye-aye swabs.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0147325},
doi = {10.1128/mra.01473-25},
pmid = {41705811},
issn = {2576-098X},
abstract = {Two circular, complete genomes of anelloviruses were identified from a crowned lemur anal swab and an aye-aye skin swab from individuals at the Duke Lemur Center (Durham, NC, USA). The anelloviruses represent two species in the Anelloviridae family and expand a developing lemur-associated anellovirus lineage.},
}

@article {pmid41577947,
year = {2026},
author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6583},
pmid = {41577947},
issn = {2045-2322},
support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.},
}

@article {pmid41705261,
year = {2026},
author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH},
title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101318},
pmid = {41705261},
issn = {2665-9271},
abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.},
}

@article {pmid41705163,
year = {2026},
author = {},
title = {Correction to: Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag020},
doi = {10.1093/ismeco/ycag020},
pmid = {41705163},
issn = {2730-6151},
abstract = {[This corrects the article DOI: 10.1093/ismeco/ycaf183.].},
}

@article {pmid41704957,
year = {2026},
author = {Zhu, J and Xia, T and Wang, L and Yin, X and Ma, Y and Shen, J},
title = {Investigating the benefits of metagenomic next-generation sequencing for patients experiencing infections after total hip replacement surgery: a retrospective cohort study with a minimum of one year of follow-up.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1735867},
pmid = {41704957},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Arthroplasty, Replacement, Hip/adverse effects ; Female ; Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis/drug therapy ; Aged, 80 and over ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Follow-Up Studies ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {OBJECTIVE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) technology in diagnosing and treating periprosthetic joint infection (PJI) following total hip arthroplasty (THA).

METHODS: From September 2018 to September 2024, 15 patients with periprosthetic infection after total hip arthroplasty were admitted. There were 11 males and 4 females; ages ranged from 28 to 87 years old, with an average of 63 years old. Infection occurred 6 to 42 months after total hip arthroplasty, with an average of 22.7 months. The infection lasted between 15 and 115 days, averaging 37.6 days. After being admitted to the hospital, joint fluid was collected for bacterial culture and mNGS. Following admission, joint fluid was collected for bacterial culture and mNGS, and antibiotics were adjusted based on the results, with surgery used to control the infection if needed.

RESULTS: Bacterial culture method was positive in 10 cases (66.7%), with a total of 12 pathogenic bacteria types detected. MNGS was positive in 15 cases (100.0%), with a total of 19 pathogenic bacteria types detected. There was a statistically significant difference in the positive rate between the two methods (P < 0.05). Out of the 10 patients, 5 who tested positive using both the bacterial culture method and mNGS test showed identical pathogenic bacterial types, resulting in a 50.0% compliance rate. The testing time (from sample delivery to results) was (3.07 ± 0.96) days for bacterial culture method and (1.67 ± 0.49) days for mNGS test, and the difference was statistically significant (t=5.03, P<0.001). The patients were followed up for 13 to 82 months, with a mean of 40.7 months. In one patient, the infection returned three months after undergoing one-stage revision surgery, while the other 14 patients showed no signs of infection, resulting in an infection control rate of 93.3%.

CONCLUSION: MNGS can detect the pathogenic bacteria of postoperative PJI after THA more quickly and accurately than the bacterial culture method, which is crucial for guiding antibiotic and surgical treatment combinations for patients with postoperative PJI after THA.},
}

Humans
Male
Middle Aged
*Arthroplasty, Replacement, Hip/adverse effects
Female
Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Prosthesis-Related Infections/microbiology/diagnosis/drug therapy
Aged, 80 and over
*Metagenomics/methods
Adult
*Bacteria/genetics/classification/isolation & purification
Follow-Up Studies
Anti-Bacterial Agents/therapeutic use

@article {pmid41704904,
year = {2025},
author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y},
title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1722274},
pmid = {41704904},
issn = {2296-861X},
abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.},
}

@article {pmid41704848,
year = {2025},
author = {Nayak, D and Behera, P and Singh, S and Tripathy, PS and Dash, SS and Dasgupta, M and Mohanty, S and Sahoo, MR and Satapathy, CR and Sasmal, A and Sahu, S},
title = {Sucrose supplementation influences gut microbial diversity and functional shifts in Apis cerana indica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733283},
pmid = {41704848},
issn = {1664-302X},
abstract = {Honeybee colonies are increasingly threatened by nutritional scarcity and biotic stressors, underscoring the need to understand the role of gut microbiota in mitigating these challenges. This study examined the gut microbial composition of Apis cerana indica under two dietary regimes: sucrose-fed and sucrose-unfed, to assess how nutrition influences microbial diversity and metabolic potential following metagenomics. Metagenomic sequencing of gut samples revealed 147,146 contigs, with the longest and shortest contigs measuring 615,154 kb and 200 kb, respectively. Comparative analysis indicated a higher relative abundance of Bacillus spp. in sucrose-fed bees, whereas Enterococcus was more dominant in unfed populations. Sucrose feeding significantly enhanced gut microbial diversity (Shannon index: 2.59; Simpson's index: 0.87) compared to unfed bees (Shannon: 1.91; Simpson: 0.68). Key genera, including Gilliamella, Bacillus, and Lactobacillus, were consistently present but showed varying relative abundances. Functional annotation via KEGG pathway analysis revealed elevated activity of glycolysis and the pentose phosphate pathway in sucrose-fed bees, with exclusive detection of key metabolic enzymes, hexokinase and enolase. Additionally, elevated sucrose metabolism and proteolytic enzyme activity were noted, reflecting enhanced metabolic versatility. Our findings highlight the importance of sucrose dietary supplementation in shaping gut microbial structure and function, their diversity, and metabolic capacity, suggesting its potential as a practical nutritional intervention to sustain honeybee health during a period of floral dearth. The outcome of the study encourages exploring the long-term ecological and physiological impacts of dietary strategies on colony resilience and productivity.},
}

@article {pmid41704809,
year = {2026},
author = {Zhang, M and Jiao, T and Li, W},
title = {Allergic bronchopulmonary aspergillosis in a patient without history of asthma: a case report.},
journal = {Medical mycology case reports},
volume = {51},
number = {},
pages = {100770},
pmid = {41704809},
issn = {2211-7539},
abstract = {Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary hypersensitivity disease triggered by Aspergillus fumigatus. While the standard first-line therapy per International Society for Human and Animal Mycology (ISHAM) guidelines is glucocorticoids or itraconazole alone, combination therapy may be used briefly for rapid symptom control. We present a 39-year-old man without asthma who presented with cough and sputum. Chest computed tomography (CT) revealed diagnostic findings of central bronchiectasis and high-attenuation mucus, later confirmed as mucus plugs by bronchoscopy. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) detected a high load of A. fumigatus. Markedly elevated total IgE, A. fumigatus-specific IgE, and eosinophils confirmed ABPA. Although initial voriconazole monotherapy failed, adding oral glucocorticoids led to rapid clinical and radiographic improvement. No recurrence was observed on CT 7 months post-treatment, reinforcing that asthma is not a prerequisite for ABPA diagnosis.},
}

@article {pmid41704794,
year = {2025},
author = {Basu, U and Ahanger, SA and Gai, X and Hu, X},
title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1749879},
pmid = {41704794},
issn = {1664-462X},
abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.},
}

@article {pmid41704740,
year = {2026},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Integrated metagenomic and metabolomic analysis reveals regional style differences in Maotai-flavour Baijiu.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100558},
pmid = {41704740},
issn = {2666-5174},
abstract = {This research focused on Maotai-flavour Baijiu from three representative production regions in the Chishui River Basin, namely Maotai Town (MT), Jinsha (JS), and Renhuai (RH). By integrating metabolomics and macrogenomics techniques, the study analyzed the differences in volatile flavor compounds and microbial community structures in the fourth-round fermented grains and base liquor. Additionally, it explored the associative mechanism between microorganisms and flavor metabolism. The findings indicate that the microbial community compositions of fermented grains vary significantly across different production areas. The production area of Maotai Town mainly consists of Saccharomyces and Lactobacillus, with the highest content of ester substances. The fungal community in Jinsha is extremely stochastic, abundant in Mucoromycota, and has elevated contents of aldehydes and phenols. The distribution of microorganisms and flavor substances in the Renhuai production area lies between the two. The sensory evaluation of the base liquor indicates that the Jinsha production area features prominent floral and fruity aromas, the Maotai Town exhibits significant sour and sauce aromas, and the Renhuai production area has a well-balanced flavor. The correlation analysis shows that yeasts such as Saccharomyces and Pichia are positively correlated with esters such as ethyl acetate, while bacteria such as Limosilactobacillus are closely associated with short-chain fatty acid metabolism. This research reveals the microbiological basis for the differences in the Maotai style among different production regions and provides a theoretical foundation for regional characteristic production and process optimization.},
}

@article {pmid41704508,
year = {2026},
author = {Sidiq, Y and Rahayu, T and Indrayudha, P and Tyastuti, EM and Althaf, AZW and Sari, BK},
title = {Metabarcoding data: Full-length 16S rRNA sequence of endophytic bacteria in the root of asymptomatic and blast-symptomatic rice plants (Oryza sativa, L.).},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112522},
pmid = {41704508},
issn = {2352-3409},
abstract = {There is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents full-length 16S metagenomic sequences of endophytic bacteria isolated from the roots of blast-infected and uninfected rice plants. Root samples were processed and subjected to surface sterilisation. Following total genomic DNA extraction, sequencing was performed using 16S ribosomal RNA primers via the high-throughput Oxford Nanopore Technologies platform. The raw sequence data were filtered for quality control using NanoFilt. Subsequently, the sequences were aligned against the National Center for Biotechnology Information (NCBI) 16S RefSeq database to identify the species of the endophytic root bacteria. The data associated with this project have been registered in the NCBI BioProject database under accession number PRJNA992961. The dataset comprises two distinct sample groups, each analysed in duplicate, with sequencing yields ranging from 17.7 to 20.3 Mb. Consequently, this dataset provides valuable insights regarding the comparative composition of endophytic bacteria inhabiting healthy roots versus those found in blast-infected rice. Characterizing this diversity, particularly within healthy rice plants, is essential for foundational research underpinning the future development of biofertilizers.},
}

@article {pmid41704501,
year = {2026},
author = {Yoshioka, Y and Ando, C and Yamashita, H and Kawamitsu, M and Kawachi, M and Tsunematsu, Y and Shoguchi, E},
title = {A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112499},
pmid = {41704501},
issn = {2352-3409},
abstract = {Increasing occurrences of toxic dinoflagellate blooms are a growing concern under climate change. The benthic dinoflagellate Ostreopsis blooms through mechanisms that remain poorly understood and is assumed to produce palytoxin-like compounds such as ovatoxins. Recent studies have highlighted the diversity of bacterial communities associated with Ostreopsis and suggested a possible role for these bacteria in toxin biosynthesis. However, genome information on potential bacterial toxin producers remains limited. Here, we report a dataset of bacterial metagenome-assembled genomes (MAGs) obtained from the culture of the toxic dinoflagellate Ostreopsis cf. ovata strain (NIES-3351). HiFi long reads from PacBio Revio system were assembled with hifiasm-meta. We identified forty complete bacterial MAGs, each with an estimated completeness of 93-100%. These MAGs span a wide range of genome sizes (1.5 Mb to 6.7 Mb) and GC contents (36% to 67%). The dataset is available at DDBJ/ENA/GenBank under accession number PRJDB37958.},
}

@article {pmid41704314,
year = {2026},
author = {Liu, Y and Xu, H and Cao, J and He, Q and Wang, N and Du, M and Zhao, Y and Dugarjaviin, M and Zhang, X},
title = {Effect of equine-derived Lactobacillus M11 on the reproductive performance of KM pregnant female mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741988},
pmid = {41704314},
issn = {1664-302X},
abstract = {INTRODUCTION: This study aimed to evaluate the effects of equine-derived Lactobacillus M11 on reproductive performance and metabolic profiles in pregnant Kunming (KM) mice. The objective was to explore the potential of M11 as a safe and effective alternative to antibiotics in antibiotic-free farming systems.

METHODS: Specific pathogen-free (SPF) female KM mice were randomly assigned to a blank control group (BC) and three intervention groups (M11-L, M11-M, M11-H). The intervention groups received daily gavage of M11 at low (1.0 × 10[7] CFU/mL), medium (1.0 × 10[8] CFU/mL), and high (1.0 × 10[9] CFU/mL) concentrations for 21 days. Host physiological parameters, metagenomic profiles, and metabolomic signatures were analyzed to assess the impact of M11 supplementation.

RESULTS: (1) Host Physiology and Biochemistry: The M11-H group exhibited a significant elevation in albumin (ALB; 40.30 ± 1.75 g/L), suggesting enhanced nutritional status or hepatic protein synthesis. The M11-L group showed transient increases in alanine aminotransferase (ALT; 59.57 ± 10.34 U/L) and total cholesterol (TC; 2.90 ± 0.24 mmol/L), indicative of adaptive hepatic lipid metabolism. (2) Microbial Community Reconfiguration: Metagenomic analysis revealed significant structural shifts in the gut microbiota between the BC and M11-H groups. Notably, the M11-H group showed enrichment of Bacillota, which correlated with "O-antigen nucleotide sugar biosynthesis," while differences in Pseudomonadota were associated with immune regulation. (3) Metabolomic Profiling: Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated clear separation in the cecal metabolome space. KEGG pathway enrichment analysis highlighted significant alterations in "glycine/serine/threonine metabolism" and "arginine/proline metabolism" pathways. (4) Integrated Multi-Omics Analysis: Correlation analysis identified a significant positive association between s_Clostridiaceae_bacterium (Bacillota) and specific metabolites (3-hydroxy-4-aminopyridine sulfate), suggesting the formation of a regulatory "gut-reproductive axis."

DISCUSSION: The results demonstrate that Lactobacillus M11 improves metabolic support during pregnancy through three primary mechanisms: modulation of the gut microbiota, activation of key metabolic pathways, and enhancement of antioxidant capacity. These findings provide a theoretical basis for the application of probiotic-mediated reproductive support in antibiotic-free farming, highlighting M11 as a promising candidate for improving livestock health and productivity.},
}

@article {pmid41704313,
year = {2026},
author = {Ramzan, F and Vassiliou, L and Tsaltas, D},
title = {Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1697953},
pmid = {41704313},
issn = {1664-302X},
abstract = {Orchids, one of the most diverse and ecologically important plant families, form complex associations with endophytic microorganisms that are vital for their survival, growth, and adaptation. These endophytes, including both fungi and bacteria, inhabit orchid tissues without causing harm and contribute to key physiological processes such as nutrient acquisition, stress tolerance, and disease resistance. This review explores the diversity and ecological roles of orchid-associated endophytes, emphasizing their significance in promoting germination, biomass production, and resilience to environmental stressors. Plant Growth-Promoting Bacteria (PGPB) such as Pseudomonas, Bacillus, and Burkholderia enhance nutrient uptake and plant defense, offering eco-friendly alternatives to chemical fertilizers and pesticides. Beyond ecological functions, endophytes show potential in biotechnology for sustainable agriculture, conservation, and novel bioactive compound discovery. Despite advances in molecular tools like metagenomics and next-generation sequencing, challenges persist in fully understanding and utilizing these microbes. This review highlights the need for multidisciplinary collaboration to optimize microbial inoculants, elucidate symbiotic mechanisms, and develop practical applications for conservation and sustainable horticulture. By integrating fundamental research with applied strategies, this work aims to unlock the full potential of orchid-associated endophytes in ecological and commercial domains.},
}

@article {pmid41704276,
year = {2026},
author = {Zhang, Y and Chen, W and Yu, X and Feng, J and Sammad, A and Wang, Z and Yin, K},
title = {Leonurine ameliorates experimental type 2 diabetes through gut microbiota remodeling, enhanced butyrate production, and MPC2 activation to restore GLP-1 secretion.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1747267},
pmid = {41704276},
issn = {1663-9812},
abstract = {The core pathophysiological mechanism of type 2 diabetes mellitus (T2DM) is closely associated with gut microbiota dysbiosis and its consequential impairment of enteroendocrine glucagon-like peptide-1 (GLP-1) secretion. T2DM mouse model was established using high-fat diet (HFD) feeding combined with streptozotocin (STZ) administration. Diabetic mice received 30 or 60 mg/kg of leonurine (LEO) via daily gavage for 12 weeks. Gut microbiota composition was profiled by metagenomic sequencing, fecal short chain fatty acids (SCFAs) concentrations were quantified via enzyme-linked immunosorbent assay (ELISA), and GLP-1 expression was assessed using oral glucose tolerance tests (OGTT), ELISA, and immunofluorescence. In vitro, high-glucose (25 mM)-challenged GLUTag enteroendocrine cells were employed to delineate the butyrate-mitochondrial pyruvate carrier 2 (MPC2) regulatory network using qPCR and Western blotting. LEO intervention significantly ameliorated glucose intolerance in diabetic mice and elevated GLP-1 levels in serum and colonic tissues. Metagenomic analysis revealed that LEO (60 mg/kg) remodeled gut microbiota structure, markedly enhancing α-diversity and specifically enriching butyrate-producing Alistipes. Mechanistically, butyrate activated MPC2 expression, effectively restoring cristae architecture defects observed by transmission electron microscopy, thereby promoting GLP-1 secretion. Crucially, MPC2 knockdown abrogated the secretagogue effect of butyrate on GLP-1 in GLUTag cells. LEO alleviates T2DM by remodeling the gut microbiota ecosystem, enhancing butyrate biosynthesis, and activating an MPC2-dependent mitochondrial energy metabolism pathway to reverse GLP-1 secretory dysfunction in intestinal L cells. This study establishes MPC2-mediated mitochondrial functional repair as a core mechanism through which microbial metabolites regulate enteroendocrine hormone secretion, identifying a novel therapeutic target within the "gut-islet axis" for diabetes intervention. Future studies should identify its active constituents, elucidate downstream effectors, and validate this mechanism in germ-free models.},
}

@article {pmid41703832,
year = {2026},
author = {Yao, X and Chen, X and Niu, J and Li, J and Li, W and Zhu, H and Li, X and Sun, B},
title = {Storage time drives divergent microbial functions and flavor metabolism in high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118363},
doi = {10.1016/j.foodres.2026.118363},
pmid = {41703832},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Taste ; *Hot Temperature ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; Metabolomics ; Time Factors ; Bacteria/metabolism/classification ; *Flavoring Agents/metabolism ; },
abstract = {Baijiu is a traditional Chinese distilled liquor, whose unique flavor highly relies on the synergistic metabolism of diverse microbial communities during the brewing process. The high-temperature Daqu (HTD) used in sauce-flavor Baijiu plays a crucial role in flavor synthesis due to its enrichment of heat-resistant functional microbiota. However, traditional techniques have limited understanding of microbial community succession and functional dynamics during Daqu storage, hindering precise quality and flavor regulation. This study systematically investigated the dynamic evolution of physicochemical indexes, microbial community structure, metabolic functions, and flavor compounds in HTD during different storage periods (1st, 3rd, and 6th months) through integrated metagenomics and GC-MS metabolomics. Results showed continuous decreases in moisture, starch, and pH during storage, while aminopeptide nitrogen and acidity peaked at the 3rd month. Esters reached their highest levels at the 1st month (YQ), alcohols peaked at the 3rd month (EQ), and aldehydes dominated at the 6th month (SQ). LEfSe analysis identified Kroppenstedtia eburnea and Paecilomyces variotii as biomarkers for YQ, Saccharopolyspora rectivirgula and Aspergillus chevalieri for EQ, and Rasamsonia emersonii for SQ. Metagenomic analysis revealed differential carbohydrate and amino acid metabolism pathways: YQ showed highest enzyme abundance for phenethyl alcohol metabolism, EQ exhibited peak enzymes for pyrazine synthesis and ethanol metabolism, while SQ demonstrated superior glucoamylase activity. In addition, maximum tetramethylpyrazine at the 3rd month and highest microbial diversity in later storage (6th month).},
}

*Food Storage/methods
*Taste
*Hot Temperature
*Alcoholic Beverages/microbiology/analysis
*Microbiota
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Metagenomics
Metabolomics
Time Factors
Bacteria/metabolism/classification
*Flavoring Agents/metabolism

@article {pmid41703795,
year = {2026},
author = {Pais, ACS and Ribeiro, TB and Coscueta, ER and Salsinha, AS and Pintado, MM and Silvestre, AJD and Santos, SAO},
title = {Phenolic compounds' impact on gut microbiota: Insights from in vitro batch fecal fermentation for composition modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118167},
doi = {10.1016/j.foodres.2025.118167},
pmid = {41703795},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Feces/microbiology ; *Fermentation ; Fatty Acids, Volatile/metabolism/analysis ; *Phenols/pharmacology/metabolism ; Prebiotics ; Flavanones/pharmacology/metabolism ; Ellagic Acid/pharmacology/metabolism ; Bacteria/drug effects/genetics/metabolism ; Male ; Adult ; Female ; },
abstract = {The relationship between phenolic compounds and gut microbiota (has been widely studied to explore the health benefits of these bioactive dietary compounds. Phenolic compounds are metabolized by gut microbiota, while also modulating its composition. However, the individual effects of these compounds on human gut microbiota remain underexplored. To address this, three phenolic compouds-ellagic acid, naringenin, and phloroglucinol-underwent in vitro batch fermentation with fecal samples from healthy donors. Samples were analyzed through 16S metagenomics sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography. Results showed that ellagic acid and phloroglucinol had prebiotic properties, producing SCFAs like acetic, propanoic, and butyric acids and promoting the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium. In contrast, naringenin was linked to the growth of pathogenic genera like Escherichia and Salmonella. This study provides valuable insights into how specific phenolic compounds influence gut microbiota composition, contributing to potential pharmaceutical or nutraceutical developments.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Feces/microbiology
*Fermentation
Fatty Acids, Volatile/metabolism/analysis
*Phenols/pharmacology/metabolism
Prebiotics
Flavanones/pharmacology/metabolism
Ellagic Acid/pharmacology/metabolism
Bacteria/drug effects/genetics/metabolism
Male
Adult
Female

@article {pmid41703237,
year = {2026},
author = {Ariyo, S and Sanusi, IO and Veerabhadrappa, K and Tenywa, MG and Olutona, GO and Onohuean, H},
title = {Deterministic and probabilistic health risk assessment of heavy metals in liquid herbal cough formulations from Western Uganda.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40622-3},
pmid = {41703237},
issn = {2045-2322},
abstract = {This study investigated the concentrations and human health risks (carcinogenic and non-carcinogenic) associated with heavy metals in liquid herbal cough formulations obtained from the Western Region of Uganda. Twelve brands of registered (government authority) herbal cough formulations from reputable pharmacies were obtained and analysed. The mixtures were acid digested prior to Atomic Absorption Spectroscopy (AAS) analysis to quantify cadmium (Cd), copper (Cu), iron (Fe), lead (Pb), nickel (Ni), and zinc (Zn) in the herbal formulations, followed by human health risk assessment, using two different approaches: deterministic and probabilistic (Monte Carlo simulation). The results showed significant variations in heavy metal concentrations, with Cu, Fe, Ni, Cd, Pb, and Zn ranging from 0.020 to 1.272, not detected (ND) to 6.734, ND to 0.129, 0.002 to 0.051, ND to 0.190, and 0.043 to 0.527 mg/L, respectively, within the World Health Organization limit (WHO). Multivariate statistical analysis revealed that anthropogenic activities were the major source of heavy metal contamination. The hazard index (HI) values obtained ranged from 7.0 × 10[-4] to 2.59 × 10[-2] in children and 6.0 × 10[-4] to 2.49 × 10[-2] in adults, indicating extremely low non-carcinogenic risk (HI < 1) of exposure to heavy metals. Similarly, the incremental lifetime carcinogenic risks (ILCRs) of Ni, Pb, and Cd for both the children and adults were below the acceptable limit of 1.0 × 10[-4], indicating no carcinogenic health risk. Moreover, the probabilistic risk assessment revealed that Pb and Cd had less than a 0.01% chance of exceeding the WHO limit (negligible risk). Findings from this study indicate that heavy metal concentrations in the brands of herbal cough formulations from Western Uganda are below the safety thresholds and are safe for consumption under realistic exposure conditions.},
}

@article {pmid41702980,
year = {2026},
author = {Paoli, JE and Aung, O and Lilak, AA and Maw, MT and Cleary, NG and Watto, E and Hassell, J and Win, YT and Thein, WZ and Evans, TS and Valitutto, M and Goldstein, T and Johnson, CK and Mazet, JA and Fleischer, R and VanTassel, N and Subramaniam, K and Anderson, BD and von Fricken, ME and Mavian, CN and Murray, S},
title = {Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38406-w},
pmid = {41702980},
issn = {2045-2322},
support = {AID-OAA-A-14-00102 , GHN-A-OO-09-0001000//United States Agency for International Development/ ; },
}

@article {pmid41702865,
year = {2026},
author = {Zhang, Z and Li, Z and Chen, X and Zu, Y and Li, S and Liang, B and Ho, SH and Wang, A},
title = {Simultaneous Trichloroacetate Dechlorination Metabolism and Nitrogen Fixation in Nitrogen-Limited Aquifers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16767},
pmid = {41702865},
issn = {1520-5851},
abstract = {Haloacetates, particularly trichloroacetate (TCAA), are pervasive contaminants, yet their biotransformation in anoxic, nutrient-limited environments remains poorly understood. Here, we elucidate a geographically widespread attenuation of haloacetates in nutrient-limited aquifers by field surveys across six Chinese provinces. Enrichment cultures metabolized TCAA as the sole carbon and energy source. Major metabolites (oxalate, acetate, CO2) indicated complete hydrolytic dechlorination accompanied by fermentation and mineralization. Isotope labeling and chemical probe studies confirmed the simultaneous occurrence of TCAA dechlorination and nitrogen fixation under fixed nitrogen-limited conditions. Integrated metagenomic, metabolomic, and transcriptional analyses demonstrated nitrogen-regulated metabolic reconfiguration. Acetyl-CoA potentially associated with TCAA metabolism may enter the TCA cycle under nitrogen-limited conditions. Dehalogenase gene (had) homologues extensively co-occurred with homologues of nitrogenase genes (nifHDK) in oligotrophic environments. Potential cross-feeding interactions among unclassified Azospira sp., Ralstonia pickettii, and Azospira inquinata mediated carbon-nitrogen intermediate exchange. This study identifies a previously unrecognized process that enables simultaneous TCAA detoxification and nitrogen acquisition in oligotrophic aquifers, thereby proposing an energy-conserving and ecologically adaptive strategy for haloacetate bioremediation.},
}

@article {pmid41702524,
year = {2026},
author = {Lips, S and Schmitt-Jansen, M and Borchert, E},
title = {Metagenomic analyses of the plastisphere reveals a common functional potential across oceans.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {395},
number = {},
pages = {127830},
doi = {10.1016/j.envpol.2026.127830},
pmid = {41702524},
issn = {1873-6424},
abstract = {Trillions of plastic particles have accumulated in the oceans, covered by microbial biofilms (termed 'plastisphere') whose functional potential remains underexplored. We evaluated as one of the first of its kind genome-resolved bacterial metagenomes of the plastisphere from the North Atlantic and North Pacific garbage patches and compared their structure and functional potential to ambient plankton. Our data revealed a characteristic genetic potential of the plastisphere with functionally equivalent traits across both oceans. We found more coding genes, bigger genomes and higher GC-content in the plastisphere in comparison to the surrounding plankton community, despite residing in the same environment, reflecting an increased metabolic capacity in the plastisphere. An analysis of 340 functional genes confirmed that the plastisphere consists of microorganisms with a higher potential for nutrient metabolism, metabolize a wider range of carbon sources, attenuate radicals, fix their own nitrogen and use alternative energy sources like anoxygenic photosynthesis. Our results suggest that the overriding factor for the high functional similarity of the plastisphere in both oceans is the habitat for biofilm formation with the potential to support mutualism and nutrient sharing making genomic streamlining as found in plankton, unnecessary. Consequently, increasing plastic pollution promotes the expansion of a new functional unit at the surface of the oligotrophic oceans with various roles in biogeochemical cycles.},
}

@article {pmid41702518,
year = {2026},
author = {Wang, X and Huo, X and Hu, H and Wang, Y and Cheng, W and Wang, Y and Sun, C and Wu, X and Chen, Y},
title = {Metagenomic mining and functional reconstitution of hexanoic acid biosynthetic enzymes from Baijiu pit bottom.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134231},
doi = {10.1016/j.biortech.2026.134231},
pmid = {41702518},
issn = {1873-2976},
abstract = {Hexanoic acid is a key flavor compound in Baijiu and a valuable platform chemical, yet its efficient biosynthesis remains challenging. To overcome the carbon chain elongation bottleneck in the reverse β-oxidation (RBO) pathway in Saccharomyces cerevisiae, this study explored the metagenomic resource of a hexanoic acid-producing microbial community from the bottom of Jiang-flavor Baijiu pit. Three enriched hexanoic acid-producing consortia were obtained, all co-producing butanoic, hexanoic, and octanoic acids. Metagenomic analysis showed that while microbial compositions differed, the consortia shared similar core functional enzymes. Further correlation analysis identified 3-hydroxyacyl-CoA dehydrogenase (HBD) and acetate CoA-transferase (CAT) as key enzymes positively correlated with hexanoic acid synthesis. These enzymes were then expressed in an engineered RBO-pathway yeast strain. Expression of CAT-1 increased butanoic and hexanoic acid production by 25% and 34%, respectively, marking the first application of CAT in enhancing chain elongation in yeast. In summary, this study innovatively identified the key enzyme CAT from the microbiota of Jiang-flavor Baijiu pit bottom and achieved efficient hexanoic acid synthesis through heterologous expression. This work not only offers a strategy for mining high-performance enzymes but also provides theoretical support and technical references for the efficient biosynthesis of hexanoic acid.},
}

@article {pmid41702480,
year = {2026},
author = {Wang, B and Jiang, Y and Li, D and Wang, C},
title = {Enhancing the diagnosis accuracy of Chlamydia psittaci infection via metagenomic next-generation sequencing.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105895},
doi = {10.1016/j.meegid.2026.105895},
pmid = {41702480},
issn = {1567-7257},
abstract = {Metagenomic next-generation sequencing (mNGS) is an innovative diagnostic technique that integrates high-throughput sequencing with bioinformatics analysis. Recently, its unbiased approach, broad pathogen coverage, and rapid turnaround have led to its expanded use in diagnosing infectious diseases. This is particularly true for atypical bacterial pathogens such as Chlamydia psittaci, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella spp., for which mNGS has demonstrated significant diagnostic utility. C. psittaci, a highly pathogenic obligate intracellular bacterium, can cause severe community-acquired pneumonia (CAP). Its virulence is attributed to unique genomic pathogenicity islands, which encode both a specialized secretion system (such as the Type III Secretion System) and effector proteins like the Chlamydial Protease-like Activity Factor (CPAF), coupled with its capacity for rapid intracellular replication. Furthermore, its close genetic similarity to C. pneumoniae complicates differentiation by standard Polymerase Chain Reaction (PCR) assays. This review examines the advancements in using mNGS to diagnose C. psittaci infections in clinical settings and discusses the remaining challenges. The excessive use of antibiotics in clinical practice is still a common problem. Through its unbiased detection, mNGS can accurately identify mixed infections, thereby providing a microbiological basis for targeted antibiotic therapy. Our compilation of case reports and studies from the last five years indicates that mNGS effectively assists clinicians in promptly adjusting antibiotic regimens and holds great potential for the clinical identification of chlamydial co-infections.},
}

@article {pmid41702469,
year = {2026},
author = {Qin, L and Wu, D and Yang, J and Song, Y and Shen, C},
title = {Macro-scale resuspension governs gene-scale mechanisms of phosphorus cycling in a shallow lake.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124040},
doi = {10.1016/j.envres.2026.124040},
pmid = {41702469},
issn = {1096-0953},
abstract = {Internal phosphorus loading from sediments is becoming a major barrier to lake restoration, yet the mechanisms governing phosphorus dynamics under sediment resuspension remain poorly understood. Using controlled laboratory experiments with sediments collected from Lake Yangcheng, we examined how disturbance intensity, frequency, and duration regulate phosphorus fractions, alkaline phosphatase activity (APA), microbial community composition, and functional gene expression. Our results revealed that low-intensity disturbance, especially under high-frequency intermittent disturbance, enhanced organic phosphorus mineralization, characterized by elevated phosphate, increased APA and strong upregulation of phoB and phoX genes. Metagenomic sequencing results further showed that these conditions supported high richness of phosphorus-solubilizing bacteria (PSB), sustaining biologically mediated conversion of organic phosphorus to bioavailable phosphate. In contrast, high-intensity disturbance shifted phosphorus dynamics toward particulate dominance, rapidly satisfying microbial phosphate demand and suppressing phosphatase expression and enzymatic mineralization. Across all disturbance treatments, Pseudomonadota remained the dominant PSB phylum, and phoB consistently exhibited the highest abundance among functional genes, underscoring their central roles in phosphorus cycling. In all, our experiments demonstrate that disturbance intensity determines whether internal phosphorus loading is governed primarily by microbial or physical processes. This study highlights that optimizing resuspension patterns, rather than simply minimizing total disturbance, may provide a more effective strategy for controlling internal loading and reducing algal bloom risk in shallow urban lakes.},
}

@article {pmid41702430,
year = {2026},
author = {Nozaki, T and Kobayashi, Y and Ikeda, M and Shigenobu, S},
title = {Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2065},
pages = {},
doi = {10.1098/rspb.2025.2484},
pmid = {41702430},
issn = {1471-2954},
support = {//Japan Society for the Promotion of Science/ ; },
mesh = {*Symbiosis ; Animals ; *Aphids/microbiology/physiology ; *Buchnera/genetics/physiology ; *Serratia/genetics/physiology ; *Genome, Bacterial ; Phylogeny ; },
abstract = {Many insects rely on obligate microbial symbioses, often involving multiple partners. Although symbiont replacement is well-documented, how newly acquired and resident obligate symbionts adapt after such events remains unclear. Here, we investigate the dual obligate symbiosis of the aphid Lachnus tropicalis, where an ancestral Serratia lineage was replaced by a newly acquired Serratia lineage while the primary symbiont Buchnera remained. Our metagenomic sequencing yielded complete genomes of Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic complementarity. Although the Serratia genome retained abundant gene sets for amino acid synthesis, it also contained pseudogenes in leucine and methionine pathways, which would be compensated for by Buchnera or the host. Comparison with Lachnus roboris, which harbours the ancestral Serratia lineage, showed that the newly acquired Serratia in L. tropicalis exhibits identical tissue localization and vertical transmission pattern, suggesting the smooth succession of the prior microniche. Notably, Buchnera in L. tropicalis exhibited a slightly more degenerated genome than its counterpart in L. roboris, indicating that symbiont replacement can accelerate gene loss even in ancient symbionts. Overall, our findings provide new insights into the dynamics of novel mutualism establishment and highlight symbiont replacement as a driver of host-symbiont co-evolution.},
}

*Symbiosis
Animals
*Aphids/microbiology/physiology
*Buchnera/genetics/physiology
*Serratia/genetics/physiology
*Genome, Bacterial
Phylogeny

@article {pmid41702408,
year = {2026},
author = {Hernández-Vázquez, A and Garcia-Arellano, H and González-Cervantes, RM and López-Pérez, M and Soto, LMH and Meza, JAC and Aguirre-Garrido, JF},
title = {Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70279},
doi = {10.1111/1758-2229.70279},
pmid = {41702408},
issn = {1758-2229},
mesh = {*Lakes/microbiology ; Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; *Hydroxybutyrates/metabolism ; Mexico ; Metagenome ; Bacterial Proteins/genetics/metabolism ; *Polyesters/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Carboxylic Ester Hydrolases/genetics/metabolism ; Polyhydroxybutyrates ; },
abstract = {Crater Lake (Isabel Island, Mexico) is a meromictic, stratified, haloalkaline system. To identify and characterise PHB depolymerases across the vertical physicochemical gradients of the lake, we analysed seven metagenomes from the water column (0-23 m), one sediment metagenome, and the genomes of two organisms (HB105m and VN105m) isolated from 5 m. Taxonomic profiles revealed vertical stratification: Actinobacteriota and Cyanobacteriota dominated surface waters, while Pseudomonadota, Bacillota, and Bacteroidota prevailed in deeper layers and sediments. Alpha-diversity indices peaked at 5 and 20 m and declined at 23 m. We identified 16 putative PHB depolymerases spanning a broader phylogenetic range than previously documented for haloalkaline ecosystems. These included homologues affiliated with Vreelandella, Thiomicrorhabdus, Chloroflexota, Candidatus Cloacimonadota, and Desulfobacterales. The structural variation observed in lipase-box motifs and signal peptides suggests functional differentiation linked to redox and oxygen gradients across depths. Phylogenetic analysis of predicted and reference enzymes showed depth-specific clustering, with extracellular depolymerases predominant in oxic layers and intracellular forms more common in microoxic-anoxic zones. Overall, our results expand the known diversity of PHB-degrading lineages in extreme environments and highlight several candidate enzymes with potential biotechnological relevance for future experimental characterisation.},
}

*Lakes/microbiology
Phylogeny
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
*Hydroxybutyrates/metabolism
Mexico
Metagenome
Bacterial Proteins/genetics/metabolism
*Polyesters/metabolism
*Microbiota
Geologic Sediments/microbiology
*Carboxylic Ester Hydrolases/genetics/metabolism
Polyhydroxybutyrates

@article {pmid41700856,
year = {2026},
author = {Zhang, R and Poulain, AJ and Pu, Q and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Grégoire, DS},
title = {Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0202825},
doi = {10.1128/aem.02028-25},
pmid = {41700856},
issn = {1098-5336},
abstract = {Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that the merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions.IMPORTANCEMethylmercury is a microbially derived neurotoxin that accumulates in the food staple rice (Oryza sativa). Mitigating the health effects of methylmercury exposure requires predicting mercury cycling dynamics in rice paddies. This task is challenging because of the complex interplay of microbial and environmental factors. Our study coupled genomic and geochemical measurements with machine learning models to identify the key biological indicators of methylmercury accumulation. We demonstrated that the abundance of methanogens and methanotrophs is a major microbial predictor of methylmercury variability. This predictive framework, which considers the interactions between these coupled microbial guilds, offers greater power than methods relying only on mercury methylation genes. These findings inform better management and remediation strategies for rice paddies, offering a path to reduce methylmercury exposure and mitigate greenhouse gas emissions.},
}

@article {pmid41700755,
year = {2026},
author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e22628},
doi = {10.1002/advs.202522628},
pmid = {41700755},
issn = {2198-3844},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; },
abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.},
}

@article {pmid41700136,
year = {2026},
author = {Hubot, N and Giering, SLC and Orel, N and Klun, K and Herndl, GJ and Hohaus, F and Lucas, CH and Tinta, T},
title = {Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20784},
pmid = {41700136},
issn = {2167-8359},
mesh = {*Scyphozoa/chemistry/metabolism ; Animals ; *Microbiota ; *Mucus/chemistry/metabolism ; Seawater/microbiology/chemistry ; Nitrogen/metabolism/analysis ; *Nutrients/metabolism ; Ecosystem ; Amino Acids/metabolism ; },
abstract = {Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish-primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)-remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h[-1] until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.},
}

*Scyphozoa/chemistry/metabolism
Animals
*Microbiota
*Mucus/chemistry/metabolism
Seawater/microbiology/chemistry
Nitrogen/metabolism/analysis
*Nutrients/metabolism
Ecosystem
Amino Acids/metabolism

@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07744-8},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
}

@article {pmid41699578,
year = {2026},
author = {Wu, H and Li, N and Yang, S and Qiu, J and Zhang, M and Wang, L and Gao, R and Wu, L and Yu, Q and Cheng, X},
title = {Prevotella denticola promotes caries by inducing oral microbial dysbiosis.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-07876-9},
pmid = {41699578},
issn = {1472-6831},
support = {82170937//the National Nature Science Foundation of China/ ; 81800955//the National Nature Science Foundation of China/ ; (No. 2025GH-YBXM-033)//External Cooperation Areas of the Key Research and Development (R&D) Program of Shaanxi Province/ ; LCB202408//the Special Project of the National Clinical Research Center for Oral Diseases/ ; },
}

@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41699270},
issn = {2058-5276},
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}

@article {pmid41699049,
year = {2026},
author = {Wu, LL and Liao, YJ and Peng, WH and Chen, LK and Huang, YC and Chen, CY and Juan, CC},
title = {FK506-binding protein-5 in high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38549-w},
pmid = {41699049},
issn = {2045-2322},
support = {108-2320-B-010-045-MY3, 110-2320-B-002-080-MY3, MOST 111-2314-B-A49-072, NSTC 112-2314-B-A49-028-MY3, NSTC 112-2740-B-A49-002, NSTC 113-2740-B-A49-003, NSTC 113-2321-B-A49-014-, NSTC 114-2321-B-A49-004 -, NSTC 114-2740-B-A49-003//Ministry of Science and Technology, Taiwan/ ; MOST 106-2320-B-010-009-MY3//Ministry of Science and Technology, Taiwan/ ; CI-110-22 and CI-111-24//Yen Tjing Ling Medical Foundation/ ; },
abstract = {A high-fat diet (HFD) alters the gut microbiota (GM), impairs metabolic efficiency, and increases gut permeability and inflammation. Obesity and insulin resistance are associated with GM dysbiosis. The GM is strongly associated with metabolic disorders and fatty liver disease. The co-chaperone protein FK506-binding protein-5 (FKBP5) regulates several vital cellular processes. Although FKBP5 has been implicated in stress-related disorders, it has not been directly linked to HFD-induced metabolic fatty liver disease. This study aimed to elucidate how FK506 binding protein 5 impairment affects the GM in HFD-induced metabolic dysfunction-associated fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD). Wild-type and FKBP5-knockout (FKKO) mice were fed a normal chow diet or a high-fat diet for 16 weeks. Mouse GM was examined using 16 S rRNA metagenomic analysis. The number of gut-liver immune cells was measured using flow cytometry. HFD-induced hepatic steatosis and inflammation were prevented in FKBP5-deficient mice. FKKO animals showed higher butyric acid levels and GM resistance to diet-induced obesity alterations according to 16 S ribosomal rRNA gene analysis and displayed an HFD-specific gut-liver immunological response that maintained gut barrier failure and mucosal immunity, which are important for GM homeostasis. FKBP5 helps the GM address inadequate immunological responses, including lower gut and liver CD11b[+]Ly6C[+] monocytes and neutrophils, and protects against obesity by improving the GM response to HFD-induced MASLD. FKBP5 protects against HFD-induced MASLD through metabolic coordination between the gut barrier and intrahepatic immunity.},
}

@article {pmid41698961,
year = {2026},
author = {Mascarenhas, AC and Kantor, RS and Thissen, J and Kok, CR and Borucki, M and Morales, C and Messenger, S and Jaing, C and Wadford, DA},
title = {Metagenomic sequencing identifies potential respiratory pathogens in PCR-negative subset of surveillance samples.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33917-4},
pmid = {41698961},
issn = {2045-2322},
support = {grant 6 Nu50CK000539//Centers for Disease Control and Prevention Epidemiology and Laboratory Capacity for Community Surveillance/ ; },
abstract = {Respiratory pathogens are a significant source of global morbidity, mortality, and economic burden, with the COVID-19 pandemic driving increased interest in and funding for respiratory disease surveillance. Syndromic panel multiplex nucleic acid amplification tests (NAATs) such as the BioFire Respiratory Panel (RP) are designed to identify the most common etiologic agents of respiratory illness. Untargeted metagenomic sequencing is a powerful tool for pathogen-agnostic detection, enabling the recovery of complete genomes for genomic epidemiology and variant tracking. In this study, we performed untargeted metagenomic sequencing of 305 samples previously negative by BioFire RP and SARS-CoV-2 testing and 26 samples that were previously positive by either of the diagnostic tests. A subset of 78 samples underwent probe-capture enrichment sequencing targeting human viruses. Using these methods, we identified human respiratory viruses in 16 of the 305 previously negative samples (5%). The most common viruses identified were Influenza C virus, Human Bocavirus, Rhinovirus A and C, and SARS-CoV-2. Consensus genomes were recovered for 14 viruses with > 90% coverage breadth, revealing closely related Bocavirus strains from neighboring counties and distinct Rhinovirus strains across samples. We also identified 21 samples with a single predominant bacterial or fungal species in the previous negative cohort. These findings underscore the challenges of identifying causal agents from multiplex NAAT-negative cases and highlight the utility of metagenomics for expanding the scope of pathogen surveillance.},
}

@article {pmid41698575,
year = {2026},
author = {Du, Y and Zhao, S and Hu, Y and Wang, X and Zhang, L and Lin, B and Wang, M and Xu, Q},
title = {Dietary selection of starters drives changes of growth performance, fermentation, hindgut microbiome, and metabolism in preweaning calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27473},
pmid = {41698575},
issn = {1525-3198},
abstract = {Early feeding of starter is an effective strategy for modulating gastrointestinal microbiota in newborn calves. However, the effects of starter nutrient composition on calf gut microbiota vary significantly. Although both fiber and starch are essential for early calf nutrition, each has distinct advantages and disadvantages. This study investigated how high-starch and high-fiber diets influence growth performance, hindgut health, and microbiota in calves. Two groups of calves were fed experimental starters with distinct nutrient compositions: a high-starch (HS, n = 8) diet containing 40.4% starch and 13.3% NDF, and a high-fiber (HF, n = 7) diet containing 18.8% starch and 30.5% NDF (DM basis). The experiment spanned calf ages 14 to 63 d, with weekly BW and body size measurements using calibrated scales and measuring tape. Serum was collected via jugular venipuncture for metabolic marker analysis. At trial end, animals were slaughtered to collect hindgut tissues and contents for immunoblotting, metagenomic sequencing, and metabolite analysis. We identified a fundamental trade-off that HS feeding shaped a Bifidobacterium-dominated enterotype, correlating with superior growth performance. In contrast, HF feeding selected for a Bacteroides-dominated, more mature microbiota and significantly enhanced gut barrier integrity by upregulating key tight junction proteins (ZO-1, Claudin-1, and E-cadherin). Multiomics integration revealed that this trade-off was underpinned by different microbial metabolic pathways. The HS hindgut was enriched in enzymes and metabolites for carbohydrate and AA fermentation, driving growth. Conversely, the HF hindgut exhibited enhanced enzymatic capacity for fiber degradation (e.g., starch phosphorylase) and a metabolic profile favoring arginine biosynthesis and acetate production, which supported barrier function. This functional divergence was further evidenced in distinct short-chain fatty acid (SCFA) profiles. The HF group exhibited significantly elevated acetate and a trend for higher total SCFA concentration, whereas the HS group showed increased branched-chain fatty acids (isovalerate) and a trend toward higher butyrate and valerate proportions. Our findings provide a mechanistic model linking dietary carbohydrate source to a fundamental choice between growth optimization and gastrointestinal health in preweaning calves, offering novel insights for targeted nutritional strategies.},
}

@article {pmid41698537,
year = {2026},
author = {Wang, D and Ren, Z and Fu, W},
title = {Research on performance differences and mechanisms of sulfur-iron composite packing materials prepared from different iron sources in nitrogen and phosphorus removal from wastewater.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134220},
doi = {10.1016/j.biortech.2026.134220},
pmid = {41698537},
issn = {1873-2976},
abstract = {To address the structural instability and limited nutrient removal of traditional fillers, this study fabricated four novel composite fillers-incorporating zero-valent iron (Fe[0]), siderite (FeCO3), pyrite (FeS2), and calcium carbonate-via a melt-encapsulation method. Batch and continuous experiments systematically revealed distinct nitrogen and phosphorus removal mechanisms and microbial architectures among these fillers. While all exhibited denitrification potential, S-FeCO3 demonstrated superior shock resistance, maintaining 78.36-94.71 % nitrogen removal and reducing sulfate accumulation by 30.92 %. Conversely, S-Fe[0] caused significant nitrite accumulation (2.83 mg/L). For phosphorus, S-FeCO3 (80.53-84.49 %) significantly outperformed S-FeS2 (70.84-78.57 %) and S-Fe[0]. Microbial analysis showed a transition from Thiobacillus dominance in S-CaCO3 to Thiobacillus-Ferritrophicum co-dominance in iron-coupled systems. At the molecular level, sulfur-iron coupling up-regulated key denitrification genes (narG, nirS, nirK, nosZ) by accelerating electron transfer and relieving Fur-mediated repression, providing a systematic strategy for filler optimization in simultaneous nutrient removal processes.},
}

@article {pmid41698498,
year = {2026},
author = {Song, Y and Li, X and Li, C and Xu, J and Liu, F and Zhao, Z and Zhong, X},
title = {A Case Study of Delayed-Diagnosed Leprosy: Advancing Diagnosis through MetaPath.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108490},
doi = {10.1016/j.ijid.2026.108490},
pmid = {41698498},
issn = {1878-3511},
abstract = {BACKGROUND: Leprosy, a chronic infectious disease caused by Mycobacterium leprae, can lead to sensory deficits, motor impairment, disability, and social stigma, imposing a dual physical and psychological burden on patients. Early diagnosis and standardized treatment are therefore crucial. Metagenomic Capture Technology for Pathology (MetaPath) is a probe-capture-based high-throughput sequencing technology for pathogen nucleic acids, which holds promise for the early detection of Mycobacterium leprae in pathological specimens.

CASE SUMMARY: A 78-year-old male presented with erythematous, scaly and pruritic plaques on his trunk and extremities for over six months, worsening in the last two months. Initial differential diagnoses, including dermatomyositis, psoriasis, and mycosis fungoides, were not confirmed by laboratory or histopathological examinations. Subsequent, MetaPath revealed the presence of Mycobacterium leprae. Further history-taking revealed a prior contact with a leprosy patient and similar, undiagnosed symptoms dating back five years. The patient was finally diagnosed with paucibacillary leprosy (borderline tuberculoid type). Following isolation, referral, and initiation of standardized multidrug therapy (rifampicin and dapsone), the patient entered a long-term follow-up phase.

CONCLUSION: MetaPath successfully detected Mycobacterium leprae, providing a definitive molecular etiological evidence for this long-term undiagnosed case. This demonstrates the key advantage of MetaPath in the early diagnosis of challenging infectious diseases.},
}

@article {pmid41698031,
year = {2026},
author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C},
title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11900},
pmid = {41698031},
issn = {1520-5118},
abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.},
}

@article {pmid41697419,
year = {2026},
author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H},
title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {177},
pmid = {41697419},
issn = {1432-0991},
support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature/growth & development ; Infant, Newborn ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Female ; Feces/microbiology ; Male ; },
abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature/growth & development
Infant, Newborn
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Female
Feces/microbiology
Male

@article {pmid41697418,
year = {2026},
author = {Hossain, A and Haque, I and Al Mamun, A and Al-Din, SMS and Ara, H and Das, TK and Rahman, MM},
title = {Physicochemical and metagenomic characterization of drinking water: Public health implications in Kushtia Municipality, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {3},
pages = {224},
pmid = {41697418},
issn = {1573-2959},
mesh = {Bangladesh ; *Drinking Water/microbiology/chemistry ; *Water Microbiology ; *Environmental Monitoring ; Water Quality ; Metagenomics ; Public Health ; RNA, Ribosomal, 16S ; Bacteria ; Water Purification ; },
abstract = {Physicochemical and bacterial contamination pose a significant threat to drinking water quality in Bangladesh, requiring comprehensive analysis. This study investigates the physicochemical and metagenomic quality of drinking water from one of four water treatment plants (WTPs) in Kushtia Municipality, Bangladesh. Water samples (n = 3) from untreated, treated, and supplied water were collected between March 1 and 7, 2025. Thirteen physicochemical parameters were analyzed using traditional methods, while bacterial load was assessed using Plate Count Agar. Microbial diversity was analyzed through metagenomic sequencing of DNA extracted using the DNeasy PowerWater Kit, targeting the 16S rRNA gene (V3-V4 region) on the Illumina MiSeq platform. Alpha and beta diversity were evaluated with Chao1, Shannon, and Simpson indices, and taxonomic and pathway analysis were performed on the Kaiju and Nephele platforms. Water quality was assessed using treatment efficiency metrics, the Water Quality Index (WQI), and the Nemerow Pollution Index (NPI). Results reveal that only three of the physicochemical parameters meet the water quality standards of Bangladesh. The WTP's cumulative efficiency metric was found to be 30.76%. The WQI indicated that all water samples were unfit for drinking. The NPI showed that eight out of thirteen physicochemical parameters significantly contribute to poor water quality. Microbial evaluations revealed high bacterial levels in untreated and supplied water samples. Alpha diversity analysis, using Shannon and Simpson indices, showed no significant differences in bacterial abundance across water types. Beta diversity analysis indicated minimal dissimilarity. Functional profiling suggested the presence of antibiotic resistance-associated pathways, with predicted beta-lactam resistance representing 24.1% in treated water and 25.0% in supplied water. The dominant phyla include Proteobacteria (38% in untreated, 39% in treated, and 42% in supplied). About 75%, 83%, and 67% of the identified bacterial species were found to be pathogenic, antibiotic-resistant, and biofilm-forming, respectively, while 58% were classified as opportunistic pathogens. These results underscore the need for improved water treatment practices and more robust monitoring systems to ensure the population can access safe drinking water.},
}

Bangladesh
*Drinking Water/microbiology/chemistry
*Water Microbiology
*Environmental Monitoring
Water Quality
Metagenomics
Public Health
RNA, Ribosomal, 16S
Bacteria
Water Purification

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
pmid = {41697296},
issn = {1615-6102},
}

@article {pmid41697036,
year = {2026},
author = {Reva, ON and Sifuna, A and Orata, F and Omolo, C and Iramiot, JS and Enright, MC and Mutshembele, A and Zhou, J and Shivoga, WA},
title = {From Lake Victoria to the Tap: Antibiotic Resistance and Pathogenic Contamination of Kisumu City Water Supply and Wastewater Network.},
journal = {Tropical medicine & international health : TM & IH},
volume = {},
number = {},
pages = {},
doi = {10.1111/tmi.70105},
pmid = {41697036},
issn = {1365-3156},
support = {GCRFNGR8\1143//UK Global Challenges Research Fund Networking/ ; NIHR163838//UK National Institute for Health and Care Research/ ; },
abstract = {Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological 'hotspots' for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.},
}

@article {pmid41697021,
year = {2026},
author = {Han, B and Wen, H and Li, Y and Wang, Y and Lv, X and Kang, M and Huang, W and Lan, Y and Tong, S and Zhang, M and Chen, D and Zhu, C and Jiang, Y and Tang, D},
title = {Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR-NF-κB axis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag028},
pmid = {41697021},
issn = {1751-7370},
abstract = {Crohn's disease (CD) is a complex chronic transmural inflammatory bowel disease. Although vedolizumab (VDZ) markedly improves clinical outcomes in CD, treatment non-response remains a significant limitation, constraining its broader utility. Elucidating the mechanisms underlying VDZ responsiveness is thus critically needed. In this research, we employed a humanized mouse model of 2,4,6-trinitrobenzene sulfonic acid-induced colitis to investigate VDZ treatment response in CD. Our findings indicate that VDZ significantly alleviated disease phenotypes in a portion of CD mice. Integrated metagenomic and metabolomic profiling identified baseline gut microbiota-derived secondary bile acids as potential predictors of VDZ efficacy. Subsequent fecal microbiota transplantation from clinical donors into pseudo-germ-free mice confirmed that gut microbial composition critically influences VDZ responsiveness. Targeted metabolomics further pinpointed lithocholic acid (LCA) as a key microbially derived metabolite correlated with therapeutic remission. Single-cell RNA sequencing also revealed that intestinal macrophages serve as pivotal mediators of LCA-driven modulation of treatment outcomes. Furthermore, transcriptomic analyses demonstrated that LCA polarizes macrophages toward an M2-resolutive phenotype via concurrent engagement of the TGR5/FXR and their downstream NF-κB pathways. Ultimately, using a conditioned medium co-culture system, we established that the regulatory effects of pro-resolutive macrophage niche on treatment response in a manner dependent on the TGR5/FXR-NF-κB axis. Taken together, our study elucidates a microbiota-immune circuit in which gut microbial metabolite LCA augments VDZ responsiveness in CD by reprogramming macrophages toward a pro-resolutive phenotype via the TGR5/FXR-NF-κB signaling network. These insights provide a mechanistic foundation for biomarker development and personalized therapeutic strategies in inflammatory bowel disease.},
}

@article {pmid41696869,
year = {2026},
author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R},
title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630563},
doi = {10.1080/19490976.2026.2630563},
pmid = {41696869},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; *Mental Disorders/microbiology ; *Brain ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics ; Female ; *Brain-Gut Axis ; Biomarkers ; },
abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.},
}

Humans
*Gastrointestinal Microbiome
*Machine Learning
*Mental Disorders/microbiology
*Brain
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Male
Metagenomics
Female
*Brain-Gut Axis
Biomarkers

@article {pmid41696622,
year = {2026},
author = {Zhu, Z and Miao, X},
title = {Research progress of metagenomic next-generation sequencing in infectious diseases of the spine: a systematic review.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361251412789},
pmid = {41696622},
issn = {2049-9361},
abstract = {BACKGROUND: Infectious diseases of the spine (IDS) cause structural destruction and abscess formation, requiring precise early diagnosis. While conventional culture methods show limited sensitivity and slow turnaround, metagenomic next-generation sequencing (mNGS) offers a promising alternative with its broader pathogen spectrum, rapid turnaround time, high detection rate, and sensitivity, showing significant advantages in the diagnosis of IDS.

OBJECTIVES: This systematic review aims to synthesize the current evidence on the advantages and clinical utility of mNGS in diagnosing and managing IDS, focusing on pyogenic and granulomatous spinal infections.

DESIGN: The systematic review conducted in accordance with PRISMA guidelines.

DATA SOURCES AND METHODS: A comprehensive literature search was performed across nine electronic databases (including PubMed, Web of Science, and Embase) from 2010 to April 2025. Studies reporting on mNGS for pathogen detection in patients with suspected or confirmed spinal infections were included. The quality of included observational studies was assessed using the STROBE checklist. Data on detection spectrum, rate, sensitivity, turnaround time, and clinical impact were extracted and synthesized narratively due to high heterogeneity.

RESULTS: Twenty-nine studies (25 retrospective studies and 4 case reports) from China were included. mNGS demonstrated a significantly broader detection spectrum, identifying common pathogens (e.g., Staphylococcus aureus, Mycobacterium tuberculosis) as well as rare and fastidious organisms that were missed by conventional methods. The pooled detection rate of mNGS (36.8%-95.5%) was consistently and significantly higher than that of culture (5.9%-59.2%). mNGS also showed superior sensitivity (39%-94.7%) compared to culture. The average turnaround time for mNGS (29-53 h) was substantially faster than for culture (2-10 days). mNGS-guided therapy was associated with improved clinical outcomes, including significant reductions in inflammatory markers.

CONCLUSION: mNGS represents a powerful diagnostic tool for IDS, offering broader detection spectrum, higher detection rate, faster turnaround time, and greater sensitivity compared to conventional methods. This enables more targeted antimicrobial therapy and improves clinical management. Challenges including high costs and difficulty in distinguishing colonization from infection remain. Future efforts should focus on technical optimization, workflow automation, protocol standardization, and outcome validation in larger prospective studies.

TRIAL REGISTRATION: CRD420251170912.},
}

@article {pmid41696361,
year = {2026},
author = {Yin, L and Xu, L and Shan, YN and He, Z and Li, Y and Chen, W},
title = {Microbiota-driven therapeutic efficacy of Hyperoside in ulcerative colitis and associated anxiety.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1734356},
pmid = {41696361},
issn = {2235-2988},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/complications ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anxiety/drug therapy ; Disease Models, Animal ; *Quercetin/analogs & derivatives/pharmacology/therapeutic use ; Male ; Cytokines/metabolism ; Colon/pathology/drug effects ; Mice, Inbred C57BL ; Molecular Docking Simulation ; Signal Transduction/drug effects ; Metabolomics ; Brain-Derived Neurotrophic Factor/metabolism ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is subtype of inflammatory bowel disease that is frequently comorbid with anxiety disorders. However, effective dual-targeting therapies are still lacking. Hyperoside (HYP), a natural flavonoid, exhibits anti-inflammatory and neuroprotective properties, yet its potential therapeutic effects on UC and associated anxiety, as well as the underlying mechanisms, remain largely unexplored.

METHODS: A murine model of DSS-induced colitis was established and treated with HYP. Disease activity was assessed through body weight, colon length, and histopathology. Anxiety-like behaviors were evaluated using open field and elevated plus maze tests. Neuroinflammation was examined through immunohistochemistry of BDNF expression and microglial activation. Gut microbiota composition was profiled by metagenomic sequencing, and metabolomic profiling was conducted using the Q300 Kit. Network pharmacology and molecular docking were employed to predict signaling pathways, which were further validated by Western blotting. Additionally, antibiotic depletion experiments were conducted to determine microbiota dependency.

RESULTS: HYP administration significantly ameliorated DSS-induced colitis, as evidenced by attenuated weight loss, restored colon length, and improved histopathology. It suppressed pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and restored intestinal barrier integrity by upregulating Mucin-2 and ZO-1. Furthermore, HYP also alleviated anxiety-like behaviors and mitigated neuroinflammation by increasing BDNF levels and suppressing microglial activation. HYP treatment also restored gut microbial homeostasis, enriching beneficial bacteria such as Enterobacter ludwigii while reducing the abundance of Enterobacter hormaechei, Escherichia coli, and Acinetobacter baumannii. Metabolomic analysis revealed that HYP significantly promoted arginine biosynthesis. Network pharmacology and molecular docking identified the MAPK, PI3K-Akt, and NF-κB pathways as potential targets, with HYP showing strong binding affinity to MAPK3, AKT1, and NFκB1. Importantly, the therapeutic effects of HYP were abolished in microbiota-depleted mice.

CONCLUSION: Our findings demonstrate that HYP effectively alleviates DSS-induced colitis and comorbid anxiety-like behaviors. Its efficacy is dependent on the gut microbiota and is associated with the restoration of microbial homeostasis, enhancement of arginine metabolism, and modulation of the MAPK/PI3K-Akt/NF-κB signaling pathways. HYP represents a promising microbiota-targeting therapeutic candidate for UC and its neuropsychiatric comorbidities.},
}

Animals
*Colitis, Ulcerative/drug therapy/microbiology/complications
Mice
*Gastrointestinal Microbiome/drug effects
*Anxiety/drug therapy
Disease Models, Animal
*Quercetin/analogs & derivatives/pharmacology/therapeutic use
Male
Cytokines/metabolism
Colon/pathology/drug effects
Mice, Inbred C57BL
Molecular Docking Simulation
Signal Transduction/drug effects
Metabolomics
Brain-Derived Neurotrophic Factor/metabolism
Anti-Inflammatory Agents/pharmacology

@article {pmid41696071,
year = {2025},
author = {Forbrigger, Z and MacDonald, T and Kulkarni, K and Stadnyk, AW},
title = {Investigating diet to control asparagine uptake as an adjunct to asparaginase treatment.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1634113},
pmid = {41696071},
issn = {2234-943X},
abstract = {Ongoing refinements of multidrug regimens, and particularly the addition of L-asparaginase, resulted in an immediate gain in survival for pediatric acute lymphoblastic leukemia patients. Yet L-asparaginase has substantial side effects which may require dose reductions or delays in subsequent doses. There are at least 3 possible sources of L-asparagine to consider when balancing blood levels with asparaginase dosing, diet, cell synthesis and bacterial synthesis. To date, there is one precedent, in mice, in which blood L-asparagine levels are reduced as a consequence of reducing consumed levels. We build on that approach in experiments aimed at testing whether long-term dietary restriction of L-asparagine and possibly gut bacteria can impact blood levels. In our experiment, 2 groups of mice received food pellets with either 4% or 0% L-asparagine. Blood and fecal metabolites and fecal bacteria were sampled over 72 days. After this accommodation period, all mice continued their diet and received a single injection of pegylated E. coli recombinant L-asparaginase. Samples for bacteria and metabolites were collected 4 and 5 days later, respectively. Neither diet had adverse effects on the general health of the mice nor did diet alone change blood L-asparagine levels. Both diets led to changes in gut bacteria. L-asparaginase depleted blood L-asparagine in mice consuming either diet. Bacteria identified in fecal pellets revealed that the microbiomes of mice in the 2 cages were different (cage effect) and remained different although metagenomic analyses of day 72 feces indicated there were no diet-dependent differences in bacterial asparaginase or asparagine synthetase. These outcomes indicate that mice recover from any short-term down regulation of blood L-asparagine due to diet and consequently the metabolic controls become complex, and the gut microbes seem to not be a great influence. Further research should include approaches to determine the source of L-asparagine in the blood while ingesting diets with no/low or high amounts of L-asparagine.},
}

@article {pmid41696028,
year = {2026},
author = {Tian, W and Petrová, E and Sakai, S and Nweze, JE and Daebeler, A and Angel, R},
title = {Cultivation and genomic characterization of novel methanogens from arid desert biocrust.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag013},
pmid = {41696028},
issn = {2730-6151},
abstract = {Methanogens are strictly anaerobic archaea capable of energy conservation by methane production, yet their presence in oxic and arid environments challenges existing paradigms. In this study, we enriched and genomically characterized seven methanogenic cultures from desert biocrusts, affiliated with the genera Methanobacterium, Methanosarcina, and Methanocella. Six of these new enrichment cultures represent new species. Nonetheless, phylogenomic analyses revealed close genetic relationships with organisms from anoxic environments, indicating the absence of an evolutionary distinction. Comparative genomics exposed diverse though non-unique repertories of antioxidant (e.g. catalase, superoxide dismutase and desulfoferrodoxin), and desiccation-resistance genes (including genes for maintaining osmotic pressure and repair of cell wall and membrane), with Methanobacterium spp possessing the lowest gene abundance and diversity for oxygen and desiccation tolerance. Nevertheless, the occurrence of a Class I methanogen such as Methanobacterium in arid soils challenges the notion that members of this class are less oxygen tolerant than Class II. Pangenome analysis further uncovered unique genes enriched in membrane-associated functions and potentially non-functional stress-related genes. Via a global metagenomic survey we find that methanogens are underdetected in dryland soils, likely due to sequencing depth limitations. Our findings highlight previously overlooked methanogen diversity and ecological plasticity in oxic and desiccated habitats, and emphasize the need for further studies to elucidate their survival strategies.},
}

@article {pmid41696023,
year = {2026},
author = {Chen, G and Jing, H and Liu, B and Zhang, J and Ou, Y and Liu, W and Tian, X and Wang, R and Yan, J and Mao, T and Yang, S and Zheng, Y and Hou, L and Dong, H},
title = {Unique phylogenies and metabolic adaptations of novel lineage III and comammox Nitrospira species from deep-sea sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag003},
pmid = {41696023},
issn = {2730-6151},
abstract = {The genus Nitrospira, which includes canonical nitrite-oxidizing bacteria (NOB) and species capable of complete ammonia oxidation (comammox), plays an important role in the global biogeochemical nitrogen cycle. Typically, lineage IV Nitrospira predominate in marine environments, and other lineages are thought to be less abundant and remain poorly characterized in oceanic systems. Here, we recovered five novel metagenome-assembled genomes (MAGs) affiliated with Nitrospira lineage II-IV from deep-sea sediments. Notably, two of these MAGs represent members of lineage III and comammox Nitrospira, respectively, suggesting the presence of previously uncharacterized lineages in the deep sea. Phylogenetic and gene locus analyses indicated that deep-sea lineage III and comammox Nitrospira form distinct evolutionary clades that diverge from their terrestrial and coastal relatives, and we therefore designate these two marine-derived groups as "lineage III clade B" and "comammox clade A4", respectively. Comparative read recruitment analyses revealed that these lineages exhibit potential pan-oceanic distribution in deep-sea sediments and waters, albeit at very low abundances. Furthermore, the identification of genes encoding amtB-type ammonium transporters (amtB), the ABC-type glycerol-3-phosphate transport system (ugpABCE), a multi-subunit Na[+]/H[+] antiporter (mnh), and betaine transporters (BetT, opuABC) suggests that these newly discovered Nitrospira species possess adaptive capabilities to thrive in oligotrophic and saline marine environments. These findings provide novel insights into the occurrence, metabolic features, and adaptation strategies of lineage III and comammox Nitrospira, expand our understanding of Nitrospira diversity in the deep sea, and offer valuable perspectives on the evolutionary history of various Nitrospira lineages.},
}

@article {pmid41696020,
year = {2026},
author = {Kim, J and Murakami, T and Toyoda, A and Mori, H},
title = {Behavioural phase transitions in the migratory locust, Locusta migratoria, are related to changes in the gut bacterial composition.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag009},
pmid = {41696020},
issn = {2730-6151},
abstract = {Locusta migratoria is a grasshopper species that can change its behaviour from solitary to gregarious. Previous studies have implicated metabolites such as serotonin and dopamine in the regulation of behavioural transition in this species. While many studies using cultured microbes have demonstrated that some microbes harbor the neuroactive metabolic potential of these neurotransmitters, the association between microbial community composition and phase transition remains poorly understood. Here, we employed 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing analyses to compare the composition of gut microbial communities of L. migratoria in different behavioural phases. We found that Serratia ureilytica was enriched in the gut of gregarious individuals in contrast to the decreased presence of Klebsiella aerogenes, one of the most abundant taxa in wild individuals. The gut microbiome of gregarious individuals was functionally characterised by enriched kynurenine and tryptophan synthesis pathways, and by reduced representation of GABA, indole, and dopamine metabolism pathways compared with that of solitary individuals. These compositional changes were consistent with the enrichment of S. ureilytica and depletion of K. aerogenes, which possess the corresponding genes. In particular, the genes for kynurenine synthesis encoded by S. ureilytica specific to the gregarious phase, are known to be involved in the tryptophan production and are associated with reduced serotonin synthesis. These results highlight a distinct shift in both the taxonomic and functional composition of the gut microbiome across behavioural phases and suggest a potential microbial contribution to the behavioural changes of L. migratoria.},
}