@article {pmid42981279,
year = {2026},
author = {Chen, J and Cheng, YQ and Fan, LP and Zhou, X and Jiang, JY and Wu, F and Liang, PW and Liu, Y and Zuo, ZL and Zhu, GX},
title = {Environmental enrichment is associated with changes in the gut microbiome and resistome of captive pythons.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0360735},
pmid = {42981279},
issn = {1932-6203},
mesh = {Animals ; *Boidae/microbiology ; *Gastrointestinal Microbiome/genetics ; Environment ; Metagenomics ; },
abstract = {Environmental enrichment is widely used to improve the welfare of captive animals, yet its effects on reptilian gut microbiota remain poorly understood. Here, we used shotgun metagenomic sequencing to investigate the gut microbiome and resistome of two captive python species: Burmese python (Python bivittatus) and reticulated python (Malayopython reticulatus), before and after environmental enrichment. We found that environmental enrichment was associated with increased α-diversity in Burmese pythons, as indicated by significantly higher ACE and observed species indices, while NMDS ordination revealed differences in the observed patterns of community composition between the two species. Pseudomonadota and Bacteroidota were dominant phyla in the gut microbiota of both python species, but their relative abundances responded differently to enrichment between hosts. Functional analyses suggested an enhanced metabolic potential in Burmese pythons, particularly in carbohydrate metabolism and environmental information processing, accompanied by increased abundance of carbohydrate-active enzymes. In addition, enrichment may influence the gut resistome, with Pseudomonadota contributing the majority of antibiotic resistance genes. Overall, our results demonstrate that environmental enrichment measures, such as dietary changes and improvements in water and air quality, are associated with changes in the gut microbiome and resistome of captive pythons in a host-dependent manner, highlighting the combined roles of diet and environmental conditions in the observed changes in the gut microbiota. These findings provide exploratory insights into the functional responses and host-microbiome evolution of reptile gut microbiota to captivity and have important implications for the management and welfare of captive animals.},
}

Animals
*Boidae/microbiology
*Gastrointestinal Microbiome/genetics
Environment
Metagenomics

@article {pmid42981365,
year = {2026},
author = {Mogire, DB and Neondo, J and Muhonja, C and Awuor, C and Mureithi, D and Ogada, S and Wekesa, TB},
title = {Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362106},
pmid = {42981365},
issn = {1932-6203},
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Kenya ; *Bacteriophages/genetics ; *Soil Microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Ralstonia/virology/genetics ; Phylogeny ; Metagenome ; *Ralstonia solanacearum/virology ; Agriculture ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum species complex is a major constraint in tomato production in Kenya, resulting in yield losses of up to 100% in heavily infested fields. This study used high-throughput shotgun metagenomic sequencing approach to characterize the rhizosphere microbiomes of tomato plants in three of the major production areas in Kenya (Kirinyaga, Kiambu, and Laikipia counties) focusing on detecting Ralstonia phage sequences. Soil samples were collected from the rhizosphere of bacterial wilt-infected tomato plants, and microbial DNA was extracted using a modified phenol-chloroform protocol and sequenced using Illumina NovaSeq platform. Taxonomic profiling revealed diverse microbial communities dominated by Actinobacteria and Proteobacteria. Four Ralstonia species were confirmed (R. insidiosa, R. pickettii, R. mannitolilytica and R. wenshanensis). Sequences similar to the R. solanacearum species complex were also detected but were too short for species-level confirmation. Metagenomic analysis detected sequences matching four previously described Ralstonia phages (RSL1, RSIBR3, Anchaing, and Cimandef). Functional annotation demonstrated abundant metabolic pathways, energy production systems, and stress response mechanisms, indicating highly adaptive microbial communities in the tomato rhizosphere. This study provides baseline data on rhizosphere microbiome composition in Kenyan tomato production systems and identifies Ralstonia phage sequences that could guide future isolation and host-range studies. If future work shows that these phages are active against Ralstonia, they could contribute to locally adapted biocontrol approaches that reduce reliance on chemical pesticides.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Kenya
*Bacteriophages/genetics
*Soil Microbiology
*Microbiota/genetics
*Metagenomics/methods
*Ralstonia/virology/genetics
Phylogeny
Metagenome
*Ralstonia solanacearum/virology
Agriculture

@article {pmid42981823,
year = {2026},
author = {Nagamine, S and Endo, N and Wu, CF and Fukushi, H and Sassa-O'Brien, Y},
title = {Molecular detection of Waddlia chondrophila in aborted bovine placental and vaginal mucus samples in Japan.},
journal = {Veterinary microbiology},
volume = {323},
number = {},
pages = {111270},
doi = {10.1016/j.vetmic.2026.111270},
pmid = {42981823},
issn = {1873-2542},
abstract = {Chlamydia-related bacteria have recently raised medical and veterinary concerns as emerging causes of abortion and pneumonia in ruminants and humans in Europe and Africa. However, these bacteria have not yet been investigated in ruminants in Japan. In this study, two species, Waddlia chondrophila and Parachlamydia acanthamoebae, were examined as potential pathogens of ruminant abortion. Vaginal mucus and placental samples were collected from 29 cows that had experienced abortion or stillbirth in Japan between August 2023 and December 2023. In real-time PCR analysis, W. chondrophila DNA was detected in both the vaginal mucus and placenta from one cow, whereas P. acanthamoebae was not detected in any individual. An 856 bp 16S rRNA sequence was obtained and identified as W. chondrophila through phylogenetic analysis. The bacterial genomic copy numbers were 3.47 × 10[4] copies/mL in vaginal mucus and 2.36 × 10[6] copies/g in placenta, indicating that the placental load was 30- to 130-times higher. This study represents the first report of W. chondrophila detection in a bovine abortion case in Japan and highlights the need for further investigation of Chlamydia-related bacteria and other pathogens affecting animal and human health.},
}

@article {pmid42981844,
year = {2026},
author = {Jeong, M and Yeo, S and Kang, D and Park, S and Hyun, Y and Jeong, SY and Shin, JH and Lee, S},
title = {Antibiotic resistance gene classes show no detectable shift despite extensive microcystin-associated river microbiome reorganization.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127235},
doi = {10.1016/j.watres.2026.127235},
pmid = {42981844},
issn = {1879-2448},
abstract = {Antibiotic resistance gene (ARG) signals can reflect increasing environmental resistance or changes in the microorganisms carrying those genes. Cyanobacterial blooms make this distinction especially important because they can reorganize entire freshwater microbial communities. We combined repeated metagenomic sampling at ten sites over eleven rounds along an 85 km Nakdong River reach with taxonomic, functional, and genome-resolved analyses and site-aware machine learning. Sampling round explained 60.9% of microbial-community variation, compared with 5.0% for site, indicating that temporal turnover dominated persistent spatial structuring. After adjusting for site, season, and water temperature, high-microcystin conditions were associated with 3,241 microbial features. None of the 18 tested ARG drug classes showed a corresponding association. The resistance-candidate inventory sums candidate annotations in representative metagenome-assembled genomes (MAGs) assigned to origin samples; drug-class profiles partition the same annotations rather than measuring sample-wide ARG abundance. Across 301 representative MAGs, candidate counts were strongly positively associated with genome size, indicating that the inventory partly reflected the microbial genomic content represented. In exploratory models, predicted resistance-candidate inventories differed between community states. High-microcystin conditions therefore coincided with extensive microbial reorganization without a detectable parallel ARG-class response. Microcystin measurements should be paired with direct ARG measurements and community profiles to track toxin hazard, resistance determinants, and microbial turnover.},
}

@article {pmid42981895,
year = {2026},
author = {Huang, C and Deng, A and Liu, W and Cong, B},
title = {Metagenome-based analysis of metal resistance potential in microbial communities from Southern Mid-Atlantic Ridge surface sediments.},
journal = {Marine genomics},
volume = {88},
number = {},
pages = {101283},
doi = {10.1016/j.margen.2026.101283},
pmid = {42981895},
issn = {1876-7478},
abstract = {Deep-sea hydrothermal sediments are enriched in transition metals that exert selective pressure on resident microbial communities. Despite the recognized influence of metal toxicity on microbial diversity, the genomic basis of metal resistance and its phylogenetic distribution in hydrothermal deposits and the surrounding sediments of the Southern Mid-Atlantic Ridge (SMAR) remain poorly understood. Here, we performed metagenomic sequencing of surface sediments collected from five SMAR stations and reconstructed 157 high- and medium-quality non-redundant metagenome-assembled genomes (MAGs) to investigate the taxonomic diversity and genome-resolved distribution of metal resistance genes (MRGs). The recovered MAGs represented 15 bacterial and archaeal phyla, with Pseudomonadota dominating the community, followed by Nitrospirota and Bacteroidota. Annotation of the recovered MAGs revealed widespread resistance potential to multiple metals, indicating that diverse metal resistance mechanisms are broadly conserved across SMAR sediments. Genome-resolved taxonomic analysis further demonstrated pronounced lineage-specific patterns of MRG distribution. Gammaproteobacteria encoded the most diverse repertoire of resistance determinants, whereas Alphaproteobacteria preferentially harbored arsenic- and mercury-resistance genes. Other taxonomic groups exhibited specialized adaptive strategies, including zinc homeostasis in Bacteroidota. Our genome-resolved analyses demonstrate that metal resistance potential in SMAR sediments is taxonomically structured distribution, reflecting differences in genomic potential among microbial lineages to hydrothermal metal enrichment. These findings expand our understanding of microbial survival strategies in deep-sea hydrothermal ecosystems and provide a genomic framework for future studies of metal cycling in the deep ocean.},
}

@article {pmid42981905,
year = {2026},
author = {Hu, J and He, Y and Cui, W and Wei, L and Li, L and Wang, L and Alwathnani, H and Rensing, C and Zhang, J},
title = {Halophyte-derived rhizosphere microbiome transplantation improves physiological homeostasis and salt tolerance in alfalfa.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128801},
doi = {10.1016/j.micres.2026.128801},
pmid = {42981905},
issn = {1618-0623},
abstract = {Halophyte-associated microbiomes are promising reservoirs of stress-adapted microorganisms, yet the consequences of transferring whole rhizosphere communities to phylogenetically distinct crops have remained unclear. Here, we evaluated rhizosphere microbiome transplantation (RMT) from Suaeda salsa to alfalfa (Medicago sativa) in a 2 × 2 factorial experiment comprising control and RMT treatments at 0 and 300 mM NaCl. Plant physiological responses were integrated with metagenomic profiling, community assembly analysis, microbial association networks, and functional gene analyses. Under salinity, RMT increased plant height, leaf area, and both shoot and root biomass, reduced shoot Na[+] accumulation, and increased the shoot K[+]/Na[+] ratio. RMT also reduced H2O2, malondialdehyde, and relative electrical conductivity while increasing antioxidant enzyme activities and osmolyte concentrations, whereas gas-exchange parameters showed no significant recovery. RMT altered rhizosphere community composition and assembly and was associated with greater network connectivity and simulated robustness. Metagenomic KO profiles showed higher relative representation of functions correlated to osmoprotection, ion transport, redox protection, and cell-envelope processes. These microbial functional shifts coincided with the physiological domains most strongly improved by RMT but did not establish direct causal microbial mechanisms. Overall, halophyte-derived RMT improved alfalfa performance under salinity, with coordinated physiological recovery accompanied by substantial reorganization of the recipient rhizosphere, supporting further evaluation of whole-community microbiome transplantation for crop production in saline soils.},
}

@article {pmid42981930,
year = {2026},
author = {Zhang, L and Luo, D and Yang, J and Yang, M and Yang, Y and Yao, R and Zhan, M and Zhang, Y and Su, Y and Wang, B and Xie, B},
title = {Viral potential to modulate antibiotic resistance gene succession through host interactions during food waste composting.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144108},
doi = {10.1016/j.jhazmat.2026.144108},
pmid = {42981930},
issn = {1873-3336},
abstract = {Composting can mitigate antibiotic resistance gene (ARG) risks, yet viral contributions to their dynamics remain unclear. Using time-series metagenomics, we investigated viral roles in ARG succession during composting of two food waste types. In both composts, ARGs followed an enrichment-decline-rebound trajectory accompanied by substrate-specific ARG-host turnover. Particularly, the maturation rebound involved the re-enrichment of high-risk ARGs, including tet(L) and lnu(G). Procrustes analysis showed significant associations of viral communities with bacterial and ARG profiles. Meanwhile, virus-host networks were organized predominantly around Firmicutes, with both temperate and lytic viral abundances correlated with ARG-host dynamics during the heating-to-thermophilic transition. Viral auxiliary metabolic genes (AMGs), annotated for central carbon metabolism, nutrient acquisition, and stress responses, may aid environmental adaptation in key ARG hosts, including Bacillus spp. Although mobile genetic elements (MGEs) provided important genetic contexts for ARG mobility, only four putative virus-mediated ARG horizontal transfer records were detected. Structural equation modelling suggested potential viral involvement through host interactions, while highlighting the importance of ARG hosts and MGEs in resistome succession. Further viral perturbation experiments are needed to clarify causal contributions in future. Overall, this study provides new insights into viral roles in resistome succession, informing resistance risk management during composting.},
}

@article {pmid42981933,
year = {2026},
author = {Si, J and Li, Y and He, J and Li, Y and Hong, P and Xie, C and Wu, Z and Lu, J and Yang, D and Meng, L and Kong, L},
title = {Enhanced removal of sulfamethoxazole by tourmaline-modified iron‑carbon substrate in constructed wetlands and underlying microbial metabolic mechanisms.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143783},
doi = {10.1016/j.jhazmat.2026.143783},
pmid = {42981933},
issn = {1873-3336},
abstract = {Tourmaline-modified iron‑carbon (Fe‑C) composite fillers were fabricated via high-temperature sintering, and their structural, electrochemical, pollutant removal and microbial response characteristics were systematically investigated. The optimal formulation was 15 wt% tourmaline with a 3:1 Fe‑C mass ratio. The optimal filler features a hierarchical porous structure, and tourmaline's spontaneous polarization mitigates iron passivation and enhances interfacial electron transfer. Static adsorption experiments demonstrated that sulfamethoxazole (SMX) adsorption onto the filler is dominated by monolayer chemisorption, with a maximum capacity of 2.91 mg/g. In a 21-day high-load static simulation system, the optimal filler achieved removal efficiencies of 84.2% for chemical oxygen demand (COD), 72.3% for total nitrogen (TN), 68.7% for total phosphorus (TP) and 84.8% for SMX, significantly outperforming pure Fe‑C, commercial Fe‑C and gravel controls. Metagenomic analysis revealed that tourmaline modification was associated with enrichment of denitrifying functional genera and key genes related to electron transport, denitrification, and SMX biodegradation. The synergistic mechanism enabled efficient pollutant removal, and continuous-flow verification over 77 days further confirmed the long-term stability of the modified filler (COD 90.8%, TN 93.3%, TP 83.3%, SMX 90.8%), demonstrating its practical potential for treating antibiotic-containing agricultural wastewater with low C/N ratios (approximately 3:1 in this study).},
}

@article {pmid42982166,
year = {2026},
author = {Zhu, W and Yu, X and Niu, S and Ge, K and Liu, H and Zhang, S and Li, M and Ming, Y and Li, T and Zhao, Z and An, X and Niu, M and Wu, K and Xie, W and He, Z and Yan, Q},
title = {Context-dependent and shared responses of the zebrafish gut microbiome to KH2PO4 enrichment.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126095},
doi = {10.1016/j.envres.2026.126095},
pmid = {42982166},
issn = {1096-0953},
abstract = {Anthropogenic phosphorus (P) enrichment is widespread in aquatic ecosystems, yet its effects on the functional potential of fish gut microbiomes remain poorly understood. We conducted a replicated 42-day experiment with zebrafish (Danio rerio), combining shotgun metagenomics with genome-resolved analyses to examine how sustained KH2PO4 exposure reshapes the gut microbiome in water-only and sediment-associated systems. Evidence for sediment-dependent modulation of microbial diversity and community composition was primarily observed during early exposure, indicating that these effects varied over time. Despite context-specific differences in functional profiles, both environmental backgrounds showed enrichment of genes or modules associated with P acquisition and turnover, selected carbon utilization pathways, energy transduction, and biosynthesis, accompanied by reduced potential for certain aromatic compound degradation and nitrate assimilation processes. Genome-resolved analyses further identified a Mycobacterium population that exhibited positive abundance responses to KH2PO4 addition in both environmental backgrounds. Its genomic traits related to P homeostasis, substrate utilization, and cellular biosynthesis provide candidate mechanistic explanations for this shared response. These findings reveal sediment-dependent responses of the zebrafish gut microbiome to extreme KH2PO4 input and identify microbial functional shifts that warrant further investigation as potential indicators of P-associated environmental disturbance.},
}

@article {pmid42982592,
year = {2026},
author = {Hessels, EW and Montoya, JV and Yuen, C and Valdiviezo-Rivera, J and Rios-Touma, B and Echevarría, G and Lujan, NK},
title = {A Museum-Curated, Voucher-Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon.},
journal = {Molecular ecology resources},
volume = {26},
number = {8},
pages = {},
pmid = {42982592},
issn = {1755-0998},
support = {//Belgian Development Cooperation/ ; //World Wildlife Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Herbert A. Fritch Family Foundation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Ecuador ; *Fishes/genetics/classification ; Museums ; Biodiversity ; DNA, Environmental/genetics ; Metagenomics/methods ; Gene Library ; },
abstract = {Environmental DNA (eDNA) metabarcoding is an emerging method that promises to expedite and improve biodiversity surveys by identifying species from the genetic material they shed into the environment. eDNA methods offer many advantages over conventional specimen-based surveys, but their effectiveness hinges on reference libraries, which for highly biodiverse regions such as the Ecuadorian Amazon are too often incomplete, inconsistently curated and disconnected from morphological voucher specimens needed to reliably identify and revise taxa. To address this gap, we collected approximately 5000 fish specimens and 1500 tissues of an estimated 311 morphologically defined species from Ecuador's Aguarico, Napo and Pastaza river basins, and built a new, rigorously curated, museum voucher-backed 12S reference library spanning 748 barcodes from over 303 species across 12 orders, 46 families and 171 genera. When tested against unknown haplotypes from concurrently collected eDNA samples, the library nearly doubled the proportion identified to species (40.0%, vs. 21.3% using GenBank). It also enabled the empirical estimation of new species-level barcode thresholds: 0.4% for the full-length barcode, 0.9% for a general vertebrate mini-barcode, and 0.6% for a fish-specific mini-barcode. By linking museum vouchers, updated taxonomy, and operational scalability, this reference library helps transform eDNA metabarcoding from an exciting possibility to a practical tool for understanding, monitoring and safeguarding Amazonian freshwater biodiversity.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Ecuador
*Fishes/genetics/classification
Museums
Biodiversity
DNA, Environmental/genetics
Metagenomics/methods
Gene Library

@article {pmid42982660,
year = {2026},
author = {You, J and Liu, Z and Li, Z and Ji, Z and Yu, J and Qu, M},
title = {Positive promotion effect of negative potential on propanethiol degradation in microbial electrolytic cells.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {},
number = {},
pages = {109488},
doi = {10.1016/j.bioelechem.2026.109488},
pmid = {42982660},
issn = {1878-562X},
abstract = {Volatile organic sulfur compounds (VOSCs) are typical odorous pollutants that are difficult to abate. The effective removal of VOSCs by microbial electrolytic cells (MECs) is a promising strategy for reducing mitigation. This work employed propanethiol (PT) as a representative contaminate and explored the performance of MEC by controlling anodic potentials at -0.4, -0.2, 0, 0.2, 0.4 V (vs. Ag/AgCl). The results indicated that the potential of -0.2 V and -0.4 V increased PT removal by 8.2% and 13.9%, while sulfate conversion rose by 6.7% and 12.6%, demonstrating the prominent enhancement of negative polarization for PT remediation. Low-negative bioanode potentials of -0.4 V and -0.2 V drove high sulfur-to-sulfate conversion of 51.2% and 45.3%, highest protein/polysaccharide ratio of 1.37 and outer-membrane c-type cytochromes content of 36.7 μmol/cm[3]. Moreover, microbial community analysis showed that the abundance of functional species of Acinetobacter sp. and Thiobacillus sp. were increased. Furthermore, the observed nanowires together with metagenomic evidence further demonstrated that negative potentials exerted positive effects on microbial electroactivity. Overall, this study elucidates bioanode potential driven PT degradation of in MECs, providing valuable implications for abatement of VOSCs via bioelectrochemical systems.},
}

@article {pmid42982859,
year = {2026},
author = {Whang, SN and Wang, X and Thomas-White, KJ and Olmschenk, G and Garza, JE and Navarro, P and Gilbert, NM},
title = {Large-scale metagenomic characterization of the vaginal microbiome and uropathogens in women with recent bacterial vaginosis and urinary tract infections.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42982859},
issn = {2041-1723},
support = {R01DK137964//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/epidemiology ; *Urinary Tract Infections/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota/genetics ; Metagenomics ; Adult ; Cross-Sectional Studies ; *Metagenome ; Young Adult ; Gardnerella/genetics/isolation & purification ; United States/epidemiology ; Escherichia coli/genetics/isolation & purification ; },
abstract = {The vaginal microbiome (VMB) influences susceptibility to urogenital infections, yet large-scale, population-based species-level metagenomic studies are rare. We analyzed cross-sectional shotgun metagenomic profiles and linked clinical metadata from 10,003 women across the United States who self-reported recent bacterial vaginosis (BV), urinary tract infection (UTI), both, or neither. Here we show that women reporting recent BV or UTI displayed distinct community structures, including higher prevalence of VALENCIA CST-IV subtypes and significantly elevated alpha diversity compared with women who reported no prior diagnosis. Species-level Gardnerella profiling revealed that multiple Gardnerella species were enriched in the recent BV group but did not differ significantly between UTI and non-UTI groups, refining prior mechanistic hypotheses. Uropathogens such as E. coli, E. faecalis, and S. saprophyticus were detectable at higher prevalence and relative abundance in women who recently experienced UTI, including among participants who reported recent antibiotic use, consistent with the possibility of residual or recurrent vaginal colonization. These findings demonstrate that microbial signatures associated with recent BV and UTI remain detectable at population scale, provide a high-resolution reference for human vaginal metagenomics, and offer new directions for prevention strategies that consider the vaginal reservoir in recurrent urogenital infections.},
}

Humans
Female
*Vaginosis, Bacterial/microbiology/epidemiology
*Urinary Tract Infections/microbiology/epidemiology
*Vagina/microbiology
*Microbiota/genetics
Metagenomics
Adult
Cross-Sectional Studies
*Metagenome
Young Adult
Gardnerella/genetics/isolation & purification
United States/epidemiology
Escherichia coli/genetics/isolation & purification

@article {pmid42983317,
year = {2026},
author = {Huang, CL and Lan, CD and Liu, Y},
title = {Disseminated Mycobacterium kansasii and Salmonella Typhimurium co-infection following iatrogenic immunosuppression: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {42983317},
issn = {1471-2334},
mesh = {Humans ; Male ; *Coinfection/microbiology/diagnosis ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis/drug therapy ; *Salmonella typhimurium/isolation & purification ; *Mycobacterium kansasii/isolation & purification ; *Salmonella Infections/microbiology/diagnosis/drug therapy ; *Immunosuppression Therapy/adverse effects ; Iatrogenic Disease ; Lymph Nodes/microbiology/pathology ; Animals ; },
abstract = {BACKGROUND: Disseminated Mycobacterium kansasii and Salmonella Typhimurium co-infection is exceptionally rare, particularly in patients without overt immunodeficiency. This case describes a unique disease progression and iatrogenic drivers in such co-infections.

CASE PRESENTATION: A 61-year-old male with uncontrolled diabetes presented with recurrent fever accompanied by axillary lymph node enlargement. Elevated inflammatory markers were noted. Brain magnetic resonance imaging (MRI) revealed a right parietal abscess with subdural empyema. Blood cultures and metagenomic Next-Generation Sequencing (mNGS) of blood and cerebrospinal fluid (CSF) confirmed Salmonella Typhimurium infection. Chest computed tomography (CT) demonstrated bilateral pulmonary inflammation. Contrast-enhanced CT/MRI of the spleen showed splenomegaly with heterogeneous enhancement and diffuse small enhancing nodules. Ultrasound revealed generalized lymph node enlargement, particularly axillary. Right axillary lymph node excision pathology, culture and mNGS confirmed Mycobacterium kansasii. The patient was diagnosed with disseminated Mycobacterium kansasii (lymph nodes, lungs, and spleen) and Salmonella Typhimurium (bloodstream, brain) co-infection. HIV testing was negative, while anti-interferon-γ autoantibodies and interferon-γ levels were within normal ranges. Clinical trajectory suggested initial Mycobacterium kansasii pulmonary and lymphatic infection, followed by Salmonella bacteremia after ingesting raw pig gallbladders. Subsequent immunosuppression (cyclosporine/prednisone) triggered disseminated co-infection (brain, lymph nodes, spleen). Prolonged antimicrobial therapy achieved remission.

CONCLUSIONS: This case describes a rare disseminated co-infection with Mycobacterium kansasii and Salmonella Typhimurium, initially presenting with non-tuberculous mycobacterium infection and subsequently complicated by salmonellosis due to raw porcine gallbladder ingestion, with dissemination of both pathogens driven by immunosuppression. It highlights the need for suspicion of atypical pathogens and cautious use of immunosuppressive therapy.},
}

Humans
Male
*Coinfection/microbiology/diagnosis
Middle Aged
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis/drug therapy
*Salmonella typhimurium/isolation & purification
*Mycobacterium kansasii/isolation & purification
*Salmonella Infections/microbiology/diagnosis/drug therapy
*Immunosuppression Therapy/adverse effects
Iatrogenic Disease
Lymph Nodes/microbiology/pathology
Animals

@article {pmid42983427,
year = {2026},
author = {Smoglica, C and Angelucci, S and Di Tana, F and Antonucci, A and Marsilio, F and Di Francesco, CE},
title = {Fecal microbiome and resistome in the long-term care of an Apennine wolf (Canis lupus italicus).},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42983427},
issn = {1746-6148},
mesh = {Animals ; *Wolves/microbiology ; Male ; *Feces/microbiology ; *Microbiota/genetics ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; },
abstract = {The Apennine wolf (Canis lupus italicus) increasingly inhabits human modified landscapes, where exposure to anthropogenic environments may influence microbial circulation and antimicrobial resistance. Wildlife Rehabilitation Centers provide opportunities to describe microbial and resistance gene profiles in animals at the human-wildlife interface; however, longitudinal shotgun metagenomic data from this subspecies during rehabilitation remain scarce. A juvenile male wolf admitted to a Wildlife Rehabilitation Center after traumatic injury and treated with multiple antibiotics was sampled at admission (T0) and after 11 months of rehabilitation (T1) in this case report. Fecal shotgun metagenomic sequencing was used to describe microbial communities, reads assigned to taxa of veterinary or public health interest, and antimicrobial resistance genes. Bacterial diversity increased from T0 to T1 with a shift from an Enterobacterales dominated profile to more diverse communities. Reads assigned to bacterial and viral taxa of potential health relevance were detected at both time points. The tools CARD-RGI identified 444 antibiotic resistance genes at T0 and 417 ARGs at T1, mainly associated with efflux pumps and β-lactamases. Genes related to Highest Priority Critically Important Antimicrobials-including mcr variants, van clusters, and oxazolidinone resistance determinants-were identified. This single-animal report provides baseline information on microbiome and resistome modification during wolf rehabilitation and suggests larger longitudinal studies and biosecurity awareness in Wildlife Rehabilitation Centers.},
}

Animals
*Wolves/microbiology
Male
*Feces/microbiology
*Microbiota/genetics
Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial/genetics
Bacteria/drug effects/genetics/classification

@article {pmid42983644,
year = {2026},
author = {El-Shahidy, SM and Zakaria, AM and Ibrahim, MA and Diab, AM},
title = {Shotgun metagenomic characterization of human adenovirus F40 and a non-cpe Clostridium perfringens strain in pediatric prolonged diarrhea: a genome-resolved case study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {42983644},
issn = {1471-2334},
mesh = {Humans ; *Diarrhea/microbiology/virology ; *Clostridium perfringens/genetics/isolation & purification/pathogenicity/classification ; *Adenoviruses, Human/genetics/isolation & purification/classification ; Feces/virology/microbiology ; Metagenomics/methods ; Phylogeny ; Shotgun Sequencing ; *Clostridium Infections/microbiology ; Child, Preschool ; Female ; Gastroenteritis/virology/microbiology ; Male ; *Adenovirus Infections, Human/virology ; },
abstract = {BACKGROUND: Viral and bacterial pathogens may be concurrently detected in pediatric gastroenteritis, yet such findings are often missed by routine diagnostic methods. Shotgun metagenomic sequencing enables comprehensive detection and genomic characterization of microorganisms present in clinical specimens, including pathogens that may not be recovered by conventional testing.

METHODS: Shotgun metagenomic sequencing was performed on a single pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements.

RESULTS: Routine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40 (HAdV-F40), showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a Clostridium perfringens strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene (cpe) but harbored a conserved histotoxic virulence profile, including cpa, pfoA, colA, hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes (tetA(P) and tetB(P)) were also identified.

CONCLUSION: This case study demonstrates the feasibility of shotgun metagenomic sequencing for comprehensive detection and genomic characterization of microorganisms present in pediatric diarrheal stool specimens, including organisms not identified by routine diagnostics. The findings are descriptive and highlight the value of metagenomics as a complementary diagnostic approach. However, no conclusions regarding pathogenic synergy, causality, or the clinical contribution of the co-detected organisms can be drawn from this single case.},
}

Humans
*Diarrhea/microbiology/virology
*Clostridium perfringens/genetics/isolation & purification/pathogenicity/classification
*Adenoviruses, Human/genetics/isolation & purification/classification
Feces/virology/microbiology
Metagenomics/methods
Phylogeny
Shotgun Sequencing
*Clostridium Infections/microbiology
Child, Preschool
Female
Gastroenteritis/virology/microbiology
Male
*Adenovirus Infections, Human/virology

@article {pmid42983860,
year = {2026},
author = {Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Yang, H},
title = {Chicken farming may influence the gut antibiotic resistome and microbiome of workers: a metagenomic analysis.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42983860},
issn = {2524-4671},
support = {25IRTSTHN038//the Program for Innovative Research Team (in Science and Technology) in University of Henan Province/ ; 82273696//the National Natural Science Foundation of China/ ; },
abstract = {In the context of the broad utilization of antibiotics in poultry breeding, an increasing number of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are accumulating in chicken feces, which presents a latent danger to workers' health. However, few studies have explored the effect of chicken rearing on the microbial flora of workers. In this study, using metagenomic analysis techniques, a panoramic view of the intestinal microbiome and resistome across 40 chickens, 31 farm workers and 23 control villagers was obtained. The results showed that the chicken gut harbored more pathogens than the human gut. ESKAPE pathogens showed a stepwise increase from villagers to workers to chickens. The level of Streptococcus pneumoniae in workers was higher than that in villagers, indicating potential pathogen exposure risks. Chickens shared more ARGs with workers than villagers. Significantly higher abundances of 125 ARGs were detected in chicken samples compared to human samples. Among these, 22 ARGs were more abundant in worker samples than in villager samples. Metagenome-assembled genome (MAG) analysis revealed that 99 ARGs were annotated in human MAGs, predominantly in Escherichia coli (43 ARGs) and Klebsiella pneumoniae (22 ARGs). Co-occurrences of ARGs and mobile genetic elements (MGEs) were observed in E. coli and K. pneumoniae, with the transposon gene tnpA being carried by multiple bacteria. Co-localization of ARGs (APH(3'')-Ib, APH(6)-Id) and MGE (IS91) in the MAG (Parasutterella gallistercoris) of workers was detected, while these two ARGs showed increasing abundance from villager to worker to chicken samples. This study indicated that chicken guts serve as important reservoirs of ARB and ARGs, which may influence the gut bacterial health of workers. Therefore, it is necessary to strengthen the management of antibiotic use in chicken farms and the health monitoring of relevant populations.},
}

@article {pmid42983896,
year = {2026},
author = {Nofinska, BA and Mizutani, S and Salim, F and Sunakawa, H and Obana, N and Shiba, S and Shinmura, K and Kotani, D and Yachida, T and Takamaru, H and Kawazoe, A and Saito, Y and Ikematsu, H and Fukuda, S and Yachida, S and Yamada, T},
title = {Gut microbial and metabolic biomarkers for early-onset colorectal cancer.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42983896},
issn = {2049-2618},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Female ; Metabolomics/methods ; China ; Male ; Japan ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Biomarkers ; Cohort Studies ; Biomarkers, Tumor/metabolism ; Age of Onset ; },
abstract = {BACKGROUND: Early-onset colorectal cancer (EO-CRC) is a growing global health challenge with poorly understood etiology. While gut microbiota and metabolites are implicated in colorectal carcinogenesis, EO-CRC-associated signatures remain poorly characterized. This study presents the first large-scale multi-omics analysis in Japan cohort to characterize gut microbial and metabolic features of EO-CRC, with cross-cohort validation in an independent China cohort.

RESULTS: We enrolled 510 participants (EO-CRC n = 120, late-onset CRC [LO-CRC] n = 282, young healthy controls [yHC] n = 59, old healthy controls [oHC] n = 49); after age- and sex-matching, 324 samples were analyzed using metagenomics, metabolomics, and quantitative polymerase chain reaction (qPCR). Fourteen species formed a shared CRC-associated microbiome core enriched in both EO-CRC and LO-CRC relative to age-matched controls, of which seven were reproducible across both Japan and China cohorts. Beyond this core, 34 and 21 species were enriched exclusively in EO-CRC and LO-CRC, respectively. Among EO-CRC-specific virulence findings, the bft gene of enterotoxigenic Bacteroides fragilis, fadA of Fusobacterium nucleatum, and bai operon genes were enriched in EO-CRC, with cross-cohort validation for fadA and bai operon, and stage-specific enrichement of deoxycholic acid at Stage 0 providing preliminary metabolomic support. Targeted clbP qPCR revealed enrichment of colibactin-producing Escherichia coli specifically in EO-CRC against a background of age-increasing carriage. Metabolomic profiling identified kynurenine enrichment and depletion of vitamin B-related metabolites (pyridoxine, riboflavin, and nicotinamide) as EO-CRC-specific findings; LO-CRC showed distinct enrichment of carnitine, succinate, and spermine with relative butyrate depletion. The choline degradation pathway was enriched specifically in EO-CRC based on Enteropathway analysis. Species-based random forest classifiers distinguished EO-CRC from controls (AUPRC = 0.828; SD = 0.013; 95% CI 0.739-0.909) and generalized robustly to an independent cohort (AUPRC = 0.817; 95% CI 0.717-0.894), substantially outperforming functional gene profiles in cross-cohort settings. Within the Japan cohort, adding metabolomics provided modest additional discriminative value.

CONCLUSIONS: These findings identify a shared CRC microbiome core reproducible across age groups and cohorts, alongside EO-CRC-specific signatures encompassing enrichment of virulence-associated genes (bft, fadA), colibactin-producing E. coli (clbP), secondary bile acid biosynthetic genes (bai operon), and choline degradation capacity, as well as distinct metabolic perturbations including kynurenine enrichment and vitamin B-related metabolite depletion. Species-based classifiers generalize well across age groups and cohorts, with metabolomics providing complementary discriminatory value. All findings represent cross-sectional associations; longitudinal studies are needed to establish temporal ordering and evaluate clinical utility as non-invasive biomarkers for EO-CRC. Video Abstract.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism
*Gastrointestinal Microbiome/genetics
Multiomics
Female
Metabolomics/methods
China
Male
Japan
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Adult
Biomarkers
Cohort Studies
Biomarkers, Tumor/metabolism
Age of Onset

@article {pmid42984583,
year = {2026},
author = {Deng, H and Chen, K and Chen, K},
title = {Case Report: Pediatric group A streptococcal toxic shock syndrome complicated by acute necrotizing tracheobronchitis requiring veno-venous extracorporeal membrane oxygenation.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1900220},
pmid = {42984583},
issn = {2296-2360},
abstract = {Group A streptococcal toxic shock syndrome (STSS) in children is uncommon and can progress rapidly to multi-organ failure. Acute necrotizing tracheobronchitis (NTB) is a rare airway complication of severe infection and has seldom been reported during extracorporeal support. We describe a previously healthy 7-year-old girl admitted with 6 days of fever and 3 h of chest tightness and dyspnea. She developed septic shock, severe pneumonia, acute respiratory distress syndrome (ARDS), disseminated intravascular coagulation (DIC), acute kidney injury, and multi-organ dysfunction. Blood and sputum cultures were negative at 48 h. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid identified Streptococcus pyogenes. Serial fiberoptic bronchoscopy was used for airway clearance and extubation assessment. Procedure records described progression from mucosal congestion to erosive necrosis with pseudomembrane-like plaques, followed by healing included broad-spectrum antimicrobials, corticosteroids, intravenous immunoglobulin (IVIG), tocilizumab, hemoperfusion, continuous renal replacement therapy (CRRT), and veno-venous extracorporeal membrane oxygenation (ECMO) from hospital days 2 to 9. Lung ultrasound during ECMO showed confluent B-lines with regional A-lines. Ultrasound images were acquired on day 3; a day-4 progress note recorded a left ventricular ejection fraction (LVEF) of 62% and mild tricuspid regurgitation. In the setting of markedly elevated troponin, these findings favored sepsis-associated myocardial injury over fulminant myocarditis. ECMO was discontinued on day 9, CRRT on day 10, and the patient was extubated on day 13 after bronchoscopy showed improved airway necrosis. She was discharged on hospital day 28, 27 days after admission. At follow-up, an intratracheal granulation-tissue lesion was excised endoscopically, and the family reported preserved neurocognitive function. Together, these findings show that NTB can complicate pediatric group A streptococcal STSS and that serial bronchoscopy may help guide ventilator and ECMO weaning; as one case without a comparison group, it does not establish which treatments were responsible for recovery.},
}

@article {pmid42984650,
year = {2026},
author = {Liu, J and Zhao, M and Xu, W and Li, S and Xue, Z and Yang, G and Gao, D and Yu, H and Lian, X and Chen, L and Zhou, L},
title = {Precursor transformation and microbial responses during compost humification regulated by wood vinegar produced at different pyrolysis temperatures.},
journal = {Frontiers in chemistry},
volume = {14},
number = {},
pages = {1912238},
pmid = {42984650},
issn = {2296-2646},
abstract = {The humification stage is a critical that determines compost quality, and the addition of functional exogenous materials is an important measure to promote this stage. Cotton-stalk-derived wood vinegar, a bioactive liquid by-product of cotton stalk pyrolysis, may regulate compost humification by modulating organic matter transformation and microbial metabolism. However, the yield of these components is significantly influenced by the pyrolysis temperature. In this study, cotton stalk wood vinegar prepared at different pyrolysis temperatures was applied as an exogenous additive in co-composting with pig manure (T300, T400, T500, and T600). The regulatory effects of the compositional differences in wood vinegar on the transformation of humification precursors and microbial community succession were investigated, thereby elucidating the chemical-biological pathways of humus formation. The results showed that, compared with the control (CK), all wood vinegar treatments significantly enhanced the humification level (p < 0.05), with the T400 treatment achieving the highest humic acid content of 23.360 g/kg on day 15 of composting. Inter-component correlation analysis and FTIR two-dimensional correlation spectroscopy (2D-COS) revealed that the T400 treatment promoted the synergistic transformation of aromatic and nitrogenous precursors and accelerated condensation and polymerization reactions. Meanwhile, the T400 treatment exhibited the highest ratio of humic-like to protein-like fluorescence components, reaching 2.88:1. Regarding microbial community succession, the T400 treatment enriched microorganisms belonging to the phyla Pseudomonadota, Actinomycetota, and Bacillota, and enhanced carbon metabolism as well as glyoxylate and dicarboxylate metabolism activities. In conclusion, cotton stalk wood vinegar prepared at 400 °C effectively improved the degree of humification in the compost by promoting precursor transformation and optimizing the microbial environment. These findings provide a theoretical basis and practical guidance for the application of biomass-derived additives in composting.},
}

@article {pmid42984758,
year = {2026},
author = {Rawat, A and Prasad, N and Rawat, P and Ahmed, S and Kumar, B and Singh, A and Nayak, T and Kushwaha, RS},
title = {Beyond solute clearance: the kidney-gut-immune-nutrition axis in hemodialysis and peritoneal dialysis and a proposed framework for integrated risk stratification.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1931760},
pmid = {42984758},
issn = {2296-861X},
abstract = {Kidney disease affects approximately ~850 million people globally, with millions dependent on dialysis as life-sustaining renal replacement therapy. While dialysis corrects solute accumulation and fluid overload, it incompletely replicates normal renal physiology and introduces its own biological stressors, perpetuating a cycle of systemic dysfunction that extends well beyond the kidney. Central to this dysfunction is the kidney-gut-immune-nutrition (KGIN) axis: a bidirectional network linking renal clearance, intestinal microbial homeostasis, immune regulation, and nutritional metabolism. In end-stage renal disease, each component of this axis is simultaneously disrupted and becomes a driver of further deterioration. Uremic toxin accumulation remodels the gut microbiome toward a dysbiotic state, characterized by depletion of short-chain fatty acid-producing organisms and expansion of pathobionts. The resulting compromise of intestinal barrier integrity permits systemic translocation of lipopolysaccharide and other microbial products, sustaining chronic low-grade inflammation and a paradoxical state of immune dysfunction marked by heightened inflammatory signaling alongside impaired pathogen defense. These perturbations converge on nutritional status, driving protein-energy wasting through catabolic cytokine signaling, anorexia, and suppression of anabolic pathways, with sarcopenia reported in several dialysis cohorts to progress at two to three fold faster than age related muscle loss. Hemodialysis and peritoneal dialysis produce distinct patterns of axis disruption: hemodialysis is characterized by intermittent toxin peaks, bioincompatible membrane-driven complement activation, and more severe dysbiosis, whereas peritoneal dialysis introduces continuous peritoneal glucose exposure and a unique local immune microenvironment, with generally slower decline in residual kidney function. These modality-specific differences translate into divergent cardiovascular, infectious, and nutritional risk profiles that are incompletely explained by traditional clinical variables. Emerging multi-omics approaches, including metagenomics, metabolomics, and high-throughput immune profiling, are beginning to characterize axis disruption with unprecedented resolution, enabling in-depth characterization of host-microbiome-immune identification of patient subgroups with distinct mechanistic signatures that cannot be captured by single domain analysis alone. To bridge this analytical capability with clinical practice, we propose the Microbiome-Immune-Nutrition (MIN) Index, a conceptual, hypothesis generating composite biomarker framework designed to synthesize data across all three axis domains and stratify patients by the severity of disruption to guide targeted, personalized interventions, which remain to be demonstrated through prospective validation studies. Therapeutic strategies targeting the axis, including dietary fiber and plant-based approaches, synbiotics, fecal microbiota transplantation, advanced dialysis modalities, and omega-3 and polyphenol supplementation, show mechanistic promise but require larger, better-designed trials with hard clinical endpoints before routine clinical adoption. Standardization of microbiome research methodology, investment in longitudinal multi-omics cohorts, and development of international collaborative consortia are research priorities that will be essential to translate mechanistic insights into improvements in survival and quality of life for patients on maintenance dialysis.},
}

@article {pmid42984913,
year = {2026},
author = {Zhao, T and Chen, R and Ma, Y and Li, G and Gu, X and Chen, Y and Sun, H},
title = {Immune checkpoint inhibitor-induced multi-organ immune damage complicated by severe pneumonia: case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2003924},
pmid = {42984913},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects ; Aged ; *Lung Neoplasms/drug therapy/complications ; *Pneumonia/drug therapy/diagnosis/etiology ; Male ; *Small Cell Lung Carcinoma/drug therapy/complications ; Antibodies, Monoclonal, Humanized/adverse effects ; Myocarditis/chemically induced ; },
abstract = {Immune checkpoint inhibitor (ICI) have substantially extended survival in patients with extensive-stage small-cell lung cancer (ES-SCLC), yet they also carry the risk of life-threatening immune-related adverse events (irAEs). Clinical experience in managing multi-organ irAEs (MO-irAEs) complicated by respiratory failure and subsequent severe pneumonia remains exceedingly scarce. Here we report a 71-year-old patient with ES-SCLC (stage IVb, with brain and splenic metastases) who, after four cycles of serplulimab plus chemotherapy, sequentially developed myocarditis, myositis, and hepatic injury. Following premature tapering of glucocorticoid therapy, the patient experienced a recurrence of ICI-related toxicity, manifesting as hypophysitis, primary hypothyroidism, and adrenal insufficiency-alongside respiratory failure-and later acquired multidrug-resistant infection during the treatment course. Through individualized moderate-dose glucocorticoids, comprehensive hormone replacement, and pathogen-directed antimicrobial therapy with eravacycline and ceftazidime-avibactam guided by metagenomic next-generation sequencing (mNGS), the infection was ultimately brought under control and multi-organ dysfunction reversed. This case underscores several key points: (1) serplulimab can precipitate multi-endocrine gland insufficiency, and severe hypothyroidism may be one of the factors contributing to the respiratory failure, mandating a high index of clinical suspicion; (2) glucocorticoid regimens should adhere to adequate initial dosing, sufficient duration, and slow tapering-abrupt discontinuation risks triggering recurrence of ICI-related toxicity; and (3) rapid, precise lower-respiratory-tract pathogen identification coupled with targeted antimicrobial therapy offers particular value in managing severe pneumonia caused by drug-resistant organisms.},
}

Humans
*Immune Checkpoint Inhibitors/adverse effects
Aged
*Lung Neoplasms/drug therapy/complications
*Pneumonia/drug therapy/diagnosis/etiology
Male
*Small Cell Lung Carcinoma/drug therapy/complications
Antibodies, Monoclonal, Humanized/adverse effects
Myocarditis/chemically induced

@article {pmid42985202,
year = {2026},
author = {Nnah, EP and Ismail, A and Abia, ALK and Essack, S and Amoako, DG},
title = {Shared resistome and mobilome signatures across One Health Escherichia coli sources.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1930054},
pmid = {42985202},
issn = {2673-7647},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge facilitated by the persistence and dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) across interconnected human, animal, and environmental compartments. Despite growing recognition of environmental reservoirs in AMR ecology, integrated resistome and mobilome studies across One Health interfaces remain limited in Africa. This study applied shotgun metagenomic sequencing to culture-derived pools of multidrug-resistant (MDR) E. coli to characterize resistome composition and mobilome signatures across human, animal, and environmental sources in uMgungundlovu District, South Africa.

METHODS: A total of 539 MDR E. coli isolates recovered from human, food-animal, wastewater, and other environmental sources were grouped into 20 source-specific pools. ARGs, plasmid-associated sequences, and MGE-associated sequences were annotated against the Comprehensive Antibiotic Resistance Database, ACLAME, and MetaStorm MGE database, respectively. Analyses included alpha diversity, Bray-Curtis dissimilarity, clustering, ordination, and permutational multivariate analysis of variance (PERMANOVA); MetaCompare prioritized pools using ARG-MGE-pathogen co-occurrence patterns.

RESULTS: Across the 20 pools, 247 distinct ARGs were detected, of which 86 (35%) occurred in at least one pool from each of the three sectors. Antibiotic inactivation and target protection were the most highly represented resistance mechanisms. ARG richness, Shannon diversity, and Simpson diversity did not differ significantly among sectors. Hierarchical clustering and ordination demonstrated substantial cross-sector overlap and within-sector heterogeneity. Nevertheless, PERMANOVA identified a significant but modest association between source sector and resistome composition (pseudo-F = 1.585, R [2] = 0.157, p = 0.022), with no significant evidence of unequal multivariate dispersion (F 2,17 = 2.498, p = 0.086). Of 1,012 plasmid-associated features, 713 (70%) occurred in at least one pool from each sector, while 232 of 975 MG E-associated features (24%) were shared. Exploratory random forest classification did not significantly outperform classification under permuted source labels (p = 0.053).

CONCLUSION: These findings reveal modest sector-associated resistome structuring alongside substantial cross-sector overlap in ARG, plasmid-associated, and MGE-associated signatures. Although the pooled data do not establish direct transmission, active mobility, or physical ARG-MGE linkage, they identify shared resistome patterns and source groups that warrant targeted, isolate-resolved and linkage-aware investigation within integrated One Health surveillance.},
}

@article {pmid42985295,
year = {2026},
author = {Li, J and Li, L and Wang, J and Liu, C and Rong, X and Yang, J and Si, G},
title = {Targeted Metagenomic Sequencing for the Rapid Diagnosis of Chlamydia Caviae Pneumonia in an Elderly Patient without Known Immunosuppression or Animal Exposure: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {648250},
pmid = {42985295},
issn = {1178-6973},
abstract = {BACKGROUND: Chlamydia caviae, a pathogen primarily causing conjunctivitis and respiratory diseases in guinea pigs, rarely infects humans. Previous human cases were mostly associated with direct contact with sick guinea pigs or occurred in immunocompromised individuals.

CASE PRESENTATION: We report a case of a 79-year-old female from Sichuan, China, without known immunosuppressive disease or therapy who presented with fever, fatigue, and left upper lobe consolidation, and was diagnosed with community-acquired pneumonia (CAP). She had no documented history of contact with guinea pigs or other pets. Empirical antibiotic therapy proved ineffective. Subsequently, probe capture-based targeted next-generation sequencing (tNGS, specifically the MetaCAP™ panel) of bronchoalveolar lavage fluid (BALF) rapidly identified C. caviae (sequence count: 1107, relative abundance: 54.50%) as the highly probable causative pathogen. Following targeted therapy with a doxycycline-moxifloxacin combination regimen, the patient's temperature rapidly normalized, achieving significant clinical and radiological improvement before discharge.

CONCLUSION: This case demonstrates that pulmonary infection caused by C. caviae can occur in individuals without known immunosuppressive conditions and without direct animal contact, raising questions about potential alternative transmission routes and zoonotic reservoirs. The early application of targeted next-generation sequencing is of critical clinical value for the precise diagnosis and prompt management of rare and elusive respiratory pathogens.},
}

@article {pmid42985334,
year = {2026},
author = {Gomes, E and Figueiredo, RJ and Mesquita, JR and Almeida, C and Araújo, D and Azevedo, NF and Castro, J},
title = {From genome to phenotype: advances, challenges and One Health perspectives in the genomic prediction of antimicrobial resistance.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1924354},
pmid = {42985334},
issn = {2235-2988},
mesh = {Phenotype ; Humans ; *Drug Resistance, Bacterial/genetics ; *Genomics/methods ; *One Health ; *Anti-Bacterial Agents/pharmacology ; *Genome, Bacterial ; *Bacteria/genetics/drug effects ; Whole Genome Sequencing ; Genotype ; },
abstract = {Whole-genome sequencing (WGS) has substantially improved the detection and surveillance of antimicrobial resistance (AMR) by enabling the rapid identification of acquired resistance genes, resistance-associated point mutations, and mobile genetic elements. However, the presence of a resistance determinant does not necessarily establish its functional contribution to the antimicrobial phenotype. This mini-review argues that a central limitation of current genotype-to-phenotype prediction is representational: multidimensional resistance architectures are frequently reduced to binary presence-absence profiles. Such representations disregard gene integrity, expression state, promoter architecture, copy number, genomic localization, regulatory topology, strain background, and within-isolate population heterogeneity. Using functionally silent determinants, pseudogenized resistance genes, inducible and dosage-dependent resistance, altered permeability and efflux, heteroresistance, and genomic-context dependence as examples, we examine how this loss of biological information can generate both false-resistant and false-susceptible predictions. We further discuss why metagenomic ARG detection cannot be directly equated with phenotypic resistance and why prediction models trained on restricted clinical populations may not generalize across species, lineages, and One Health compartments. Moving from determinant detection toward context-aware and quantitative phenotype prediction will require the selective integration of long-read sequencing, transcriptomics, copy-number analysis, population-aware sequencing, standardized phenotypic metadata, and externally validated computational models. The relevant unit of AMR prediction is therefore not the resistance gene alone, but its functional state within a specific genomic, cellular, population, and environmental context.},
}

Phenotype
Humans
*Drug Resistance, Bacterial/genetics
*Genomics/methods
*One Health
*Anti-Bacterial Agents/pharmacology
*Genome, Bacterial
*Bacteria/genetics/drug effects
Whole Genome Sequencing
Genotype

@article {pmid42985422,
year = {2026},
author = {Zhang, B and Bao, J and Zhang, Z and Sun, Z and Zhang, F and Zhang, M},
title = {Rhizophagus clarus and phosphorus co-regulate oat rhizosphere metabolome-microbiome under drought: a candidate hub metabolite perspective.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1984943},
pmid = {42985422},
issn = {1664-462X},
abstract = {The interaction between arbuscular mycorrhizal fungi (AMF) and phosphorus (P) availability could enhance plant drought tolerance. Yet whether this interaction modulates nutrient uptake and grain yield in oat by reshaping rhizosphere metabolite and microbial networks remains unresolved. A pot experiment was conducted across three relative water contents (75%, 55%, and 35% relative water content, designated WW, MDS, and SDS), two AMF treatments, and three P levels (0, 40, and 80 mg kg[-][1] soil, designated P0, P1, and P2). Untargeted metabolomics and metagenomics were applied to characterize rhizosphere metabolite profiles and bacterial community structure, and to assess their relationships with nitrogen (N) and P status in the plant-soil system, grain yield and β-glucan. Drought significantly reduced grain yield, whereas moderate drought increased β-glucan accumulation; the beneficial effects of AMF on both traits were strongly modulated by soil P level. Under drought, AMF inoculation and P addition synergistically promoted N and P accumulation across oat organs; relative to P0AMF, P2AMF significantly elevated total N and P concentrations in roots, stems, leaves, panicles, and grains. Water availability was the dominant driver of rhizosphere metabolome and bacterial community variation. Under drought, AMF-P interaction further enriched rhizosphere metabolites, including amino acids and derivatives, organic acids, and benzene and substituted derivatives, while shifting the signature bacterial taxa toward Pseudomonadota (P1AMF) and Myxococcota and Gemmatimonadota (P2AMF). Network analysis identified isopentenyl pyrophosphate (IPP) as a highly connected hub metabolite, exhibiting the strongest associations with N and P nutrition, grain yield, β-glucan, and bacterial community composition. Exogenous IPP application significantly increased oat plant height, stem dry weight, and average root diameter under drought and markedly elevated the relative abundances of several rhizosphere bacterial taxa. Collectively, these findings indicate that AMF inoculation combined with P addition is associated with restructuring of the rhizosphere metabolite-microbe network under drought, and that IPP represents a candidate metabolite that warrants further investigation in these plant-microbe-soil interactions. This study provides a correlative framework linking this dual strategy to shifts in rhizosphere microbial communities and crop yield and functional quality under water-limited conditions, although mechanistic validation will require future experimental work.},
}

@article {pmid42985544,
year = {2026},
author = {Zhao, T and Sun, Y and Jiang, X and Feng, Y and Ding, J and Li, X and Deng, A},
title = {Structural characteristics and regulatory mechanisms of the ocular surface microbiota and their relationship with ocular surface health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938863},
pmid = {42985544},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Eye/microbiology/immunology ; Host Microbial Interactions ; Animals ; RNA, Ribosomal, 16S/genetics ; Meibomian Glands/microbiology ; },
abstract = {This review delineates the spatial distribution of ocular surface microbiota (OSM) and its dynamic interplay with ocular health. Culture-independent surveys employing 16S rRNA and metagenomic sequencing reveal an ultra-low-biomass ecosystem characterized by restricted α-diversity. Firmicutes, Actinobacteria and Proteobacteria are the dominant phyla. Corynebacterium, coagulase-negative staphylococci, Propionibacterium and Streptococcus show high prevalence and temporal stability. These four genera form a conserved core. Their relative abundance is continuously reshaped by geography, lifestyle, age, sex, delivery mode, contact lens wear and systemic diseases such as dry eye and diabetes. Emerging evidence implicates host-microbe crosstalk, encompassing Toll-like receptor (TLR) and NOD-like receptor (NLR) mediated sensing of pathogen-associated molecular patterns (PAMPs), secretory immunoglobulin A (SIgA) neutralization, and a putative gut-eye immunoregulatory axis, in ocular immune maturation and the maintenance of immune homeostasis, although direct causal relationships remain to be established. Under physiological conditions, competitive exclusion and negative feedback maintain microbial equilibrium. However, surgical trauma, antibiotics or corticosteroids have been associated with destabilization of this niche, under which commensals may acquire virulence genes, form biofilms and transition into opportunistic pathogens implicated in infectious keratitis, exacerbation of meibomian gland dysfunction and increased dry eye severity. Consequently, high-resolution profiling of OSM composition and function may help clarify disease mechanisms and holds promise for furnishing microbial biomarkers for precision diagnosis and personalized therapeutic intervention.},
}

Humans
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Eye/microbiology/immunology
Host Microbial Interactions
Animals
RNA, Ribosomal, 16S/genetics
Meibomian Glands/microbiology

@article {pmid42986108,
year = {2026},
author = {Xu, Y and Zhang, C and Wu, Y and Zhuo, J and Shen, X and Zhou, Y and Jin, J},
title = {Metagenomic insights into the avian gut microbiome: novel viruses, antimicrobial resistance, and beyond.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234326},
doi = {10.1128/mbio.02343-26},
pmid = {42986108},
issn = {2150-7511},
abstract = {Birds play crucial roles in shaping ecosystems, and their gut microbiomes significantly influence host physiology and pathology. Understanding the composition, functions, and dynamics of avian gut microbiomes is therefore essential. Recent advances in metagenomic and metatranscriptomic sequencing have greatly increased our ability to characterize the avian gut microbiome. This review presents a systematic summary of the current knowledge regarding the composition of the avian gut microbiome as revealed through high-throughput sequencing technologies. It provides a statistical overview of the predominant bacterial and viral taxa present in the gut microbiomes of 195 bird species, revealing a persistent trend toward the discovery of novel viruses, and gives insight into the gene functions of these taxa. Interestingly, in terms of both antimicrobial resistance and multidrug resistance, wild birds harbor a greater diversity of resistance types than poultry. This review also presents a discussion of the relationships of avian life stages and the living conditions of birds with the gut microbiome and highlights practical applications of microbiome regulation in poultry production. Building on this foundation, future research priorities are outlined, such as the study of archaea, fungi, protists, and novel viruses, ways of improving methods to reduce costs and standardize protocols, and the development of more extensive metagenomic and metatranscriptomic data resources. Ultimately, these efforts could provide a holistic understanding of the avian gut microbiome.},
}

@article {pmid42986127,
year = {2026},
author = {Massot, M and Wimmer, L and Moussawi, MA and Hamet, J and Parac-Vogt, T and Rajkovic, A and Dailey, L-A and Callens, M and Bedhomme, S},
title = {The attachment rate of Vibrio anguillarum to microplastics strongly varies with strain identity, particle characteristics, and environmental conditions.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0168726},
doi = {10.1128/aem.01687-26},
pmid = {42986127},
issn = {1098-5336},
abstract = {Microplastics (MPs), resulting from plastic objects and waste degradation, are increasingly abundant, particularly in marine environments. They exhibit a hydrophobic surface on which biofilms form easily. Metagenomic analyses of these biofilms have revealed that they often contain bacterial species potentially pathogenic to humans or animals. For this reason, MPs are suspected to present a risk to public health by acting as a vector for pathogenic bacterial species. To better understand this hazard, we studied different factors potentially affecting the bacterial attachment rate to MPs. Focusing on the fish pathogen Vibrio anguillarum, a collection of 16 GFP-labeled strains was assembled, including isolates from infected fish. Their attachment rates were measured using fluorescence microscopy on three types of MPs (milled polypropylene and polyethylene terephthalate particles, and commercially available polystyrene beads). A strong effect of the particle type was found, with higher attachment rates on milled particles, whose surface appeared qualitatively rougher based on visual examination of scanning electron microscopy images. Our results also revealed an intraspecific variation in attachment rate, highlighting the need for testing several strains of the same species to assess attachment rate and related hazards. Finally, it was observed that when a biofilm had formed by field incubation of the MPs, the differences in attachment rates between particle types were erased. The attachment of V. anguillarum depends on a combination of strain-related factors, particle characteristics, and environmental conditions, highlighting the need to combine microbiology, materials science, and environmental sciences to achieve a comprehensive risk assessment associated with MPs.IMPORTANCEMicroplastics (MPs) are increasingly abundant, particularly in marine environments. They are suspected to present a risk to public health by acting as a vector for pathogenic bacterial species. Focusing on the fish pathogen Vibrio anguillarum, we measured the attachment rates of 16 strains on three types of microplastics (milled polypropylene and polyethylene terephthalate particles, and commercially available polystyrene beads). This study highlights a strong effect of the particle type, with higher attachment rates on irregular particles, as well as a strong intraspecific variation. In a second experiment, it was observed that when a natural marine biofilm had already formed on the microplastic particles, differences in attachment rates between particle types were erased. Our findings emphasize the importance of accounting for multiple factors when assessing the risks of MPs as carriers of pathogenic bacteria, with our study addressing the first step of the conceptual pathway linking attachment, persistence, transport, exposure, and ultimately infection.},
}

@article {pmid42986371,
year = {2026},
author = {Meeto, C and Chanworawit, K and Lueangjaroenkit, P and Srinoi, P and Deevong, P},
title = {Decolorization and detoxification of aniline blue dye by Cloacibacterium normanense Gsp-T3 newly isolated from amphipods: Novel of bacterial community composition, synthetic dye-degrading bacteria, ligninolytic potential, and biodegradation pathway.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42986371},
issn = {1573-0972},
mesh = {Animals ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; *Coloring Agents/metabolism ; Phylogeny ; *Aniline Compounds/metabolism ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Laccase/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Peroxidases/metabolism ; },
abstract = {Synthetic dye contamination negatively affects ecological creatures and health because of the durability and toxicity of dye molecules. This study aimed to isolate dye-degrading bacteria from three amphipod species, comprising Floresorchestia amphawaensis (FA), Quadrivisio meufong (QM), and Grandidierella sp. (Gsp), and assess the potential of natural bacterial isolates for dye decolorization and detoxification. Based on analysis of 16S rRNA gene sequences, six novel strains that decolorize a wide range of dyes were closely related to Stenotrophomonas nitritireducens (isolate FA-T13), Isoptericola nanjingensis (FA-T16), Klebsiella quasipneumoniae (QM-T13), Acidovorax temperans (QM-T15), Bacillus subtilis group (QM-T27), and Cloacibacterium normanense (Gsp-T3). Among them, the promising strain C. normanense Gsp-T3 had the highest decolorization capability of 60.51% for a harmful triphenylmethane dye, aniline blue, and demonstrated the highest activity of ligninolytic enzymes, including laccase, manganese peroxidase, and lignin peroxidase. Decolorization by Gsp-T3 was monitored using UV-Vis spectral and HPLC analyses, and the products derived from dye biodegradation were analyzed using FTIR and GC-MS analyses. Eight degradation products were identified as aromatics, short-chain aliphatic acids, and aliphatic alcohol, and a degradation pathway of aniline blue by Gsp-T3 was proposed. Moreover, alterations in bacterial cell surface morphology were detected by SEM. In detoxification assays, the biodegradation products had a reduced cytotoxicity effect on Vero cells and did not elevate phytotoxicity (mung bean, and rice). As culture-independent method, 16 S rRNA metagenomic analysis revealed diverse amphipod-associated bacterial communities, containing several genera potentially involved in pollutant biodegradation. The findings provided knowledge of amphipod-associated bacteria and their capability for synthetic dye bioremediation.},
}

Animals
Biodegradation, Environmental
RNA, Ribosomal, 16S/genetics
*Coloring Agents/metabolism
Phylogeny
*Aniline Compounds/metabolism
*Bacteria/classification/isolation & purification/genetics/metabolism
Laccase/metabolism
Lignin/metabolism
DNA, Bacterial/genetics
Peroxidases/metabolism

@article {pmid42976626,
year = {2026},
author = {Zhang, A and Li, N and Zhang, W and Huo, X and Zhang, R and Zhou, Y and Zhou, J and Song, J and Wang, M and Zheng, Y},
title = {Aeration rate regulates organic acid metabolism during cereal vinegar solid-state fermentation: Insights from quantitative metagenomics and targeted metabolomics.},
journal = {Food chemistry},
volume = {532},
number = {Pt 4},
pages = {151838},
doi = {10.1016/j.foodchem.2026.151838},
pmid = {42976626},
issn = {1873-7072},
abstract = {Aeration is a critical parameter regulating organic acid metabolism during cereal vinegar fermentation, but its regulatory mechanism remains unclear. We integrated absolute and relative quantitative metagenomics with targeted metabolomics to elucidate how aeration affects microbial metabolism and organic acid formation. Bacterial abundance in the L, M, and H groups declined from 2.80-2.98 × 10[11] to 7.93 × 10[9]-1.97 × 10[10] copies/ng DNA, whereas fungal abundance declined from 6.02-6.67 × 10[9] to 7.90 × 10[6]-4.56 × 10[9] copies/ng DNA. Relative quantification suggested increases in microbial relative abundance, whereas their absolute abundances decreased sharply during fermentation. Aeration was associated with changes in microbial community and functional gene abundance. Subsequent acid accumulation may further influence microbial succession. Phased aeration enabled targeted modulation of organic acid profiles. In the L-H-M group, succinic acid and GABA increased by 5.89-10.29% and 7.66-13.31%, respectively, compared with constant-aeration groups. These findings provide a basis for precise control of organic acid profiles through stage-specific aeration.},
}

@article {pmid42976630,
year = {2026},
author = {Naderi, M and Sadidi, R and Besharati, R and Kebriae, A and Azimian, A},
title = {Nucleic acid amplification testing for obligate intracellular and cell wall-deficient bacteria: from assay performance to clinical interpretation, a structured narrative review.},
journal = {Diagnostic microbiology and infectious disease},
volume = {117},
number = {1},
pages = {117721},
doi = {10.1016/j.diagmicrobio.2026.117721},
pmid = {42976630},
issn = {1879-0070},
abstract = {Obligate intracellular bacteria (Rickettsia, Orientia, Ehrlichia, Anaplasma, Coxiella, Chlamydia) and cell wall-deficient Mycoplasma species present profound diagnostic challenges due to their fastidious growth, low circulating burden, and genomic instability. Nucleic Acid Amplification Tests (NAATs) have revolutionized detection, yet critical gaps persist in distinguishing active infection from persistent DNA, standardizing cycle threshold interpretation, and integrating host-response biomarkers. This structured narrative review provides a comprehensive analysis of the complete diagnostic armamentarium for these pathogens. It is based on a reproducible, non-systematic literature survey and is not a PRISMA-compliant systematic review. We cover conventional methods (culture, serology), NAAT platforms (qPCR, digital PCR, isothermal amplification), and emerging technologies including CRISPR-Cas diagnostics, metagenomic sequencing, nanopore sequencing, biosensors, and host-response biomarker profiling. We introduce four conceptual frameworks: the "biological noise" paradigm reframing low-copy detection as a signal-to-noise challenge; a temporal-dynamic algorithm accounting for pathogen-specific detection windows; the "detection-disease disconnect" emphasizing clinical contextualization of NAAT positivity; and multi-analyte integration combining NAAT with viability markers and host inflammatory signatures. We also position these frameworks relative to prior diagnostic-interpretation theories, including STARD, QUADAS-2, MIQE, Bayesian pretest-posttest reasoning, Ct-value interpretation guidance, and host-response classifier frameworks. We compare ten clinically significant pathogens across technical and biological parameters, evaluate point-of-care deployment strategies, and address antimicrobial resistance testing. Performance metrics are presented as context-dependent estimates rather than fixed constants. The next frontier lies not in incremental assay improvements but in system-level integration of pathogen detection, viability assessment, host-response profiling, and clinical phenotyping, supported by artificial intelligence-enhanced interpretation and global standardization efforts.},
}

@article {pmid42976655,
year = {2026},
author = {Zhang, B and Li, Y and Du, C and Xiong, Y},
title = {Environmental constraints reveal condition-dependent advantages of a defined benzene-degrading consortium.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144093},
doi = {10.1016/j.jhazmat.2026.144093},
pmid = {42976655},
issn = {1873-3336},
abstract = {Benzene-contaminated soils remain difficult to remediate because bioaugmentation strategies often rely on selecting individual strains with high degradation activity, while their long-term performance under environmental constraints is uncertain. Here, we show that a defined three-member consortium sustained benzene removal more effectively than the strongest degrader alone under environmental constraints. By integrating field microbiome analysis, [13]C-benzene DNA stable isotope probing, genome-resolved metagenomics, cultivation, defined consortia, isotope labeling, and long-term soil incubation, we identified and reconstructed a functional benzene-degrading consortium. Field profiling identified a limited set of taxa associated with benzene contamination. DNA-SIP, genome-resolved metagenomics, and isolate assays further differentiated the roles of the focal lineages. Stutzerimonas showed the strongest benzene degradation, Rhodococcus encoded additional aromatic-catabolic potential, and Rhizobium exhibited nitrogenase activity. Although Stutzerimonas showed the highest degradation efficiency in monoculture (approximately 78%), the three-member consortium displayed a stronger advantage under environmental constraints. When the exogenous nitrogen source was omitted, corrected degradation reached approximately 73% in the three-member consortium, compared with approximately 38% in the Stutzerimonas-Rhodococcus consortium. At 700 mg L[-1] benzene, the three-member consortium retained approximately 86% corrected degradation, whereas Stutzerimonas alone declined to approximately 44%. During 6 months of repeated benzene amendment in soil, the consortium maintained rapid benzene removal together with continued detection of all three focal bacterial lineages. These findings show that the benefit of the consortium depended on environmental context and provide a basis for evaluating candidate inocula for benzene remediation.},
}

@article {pmid42976696,
year = {2026},
author = {Wan, R and Ge, L and Zheng, ZZ and Zheng, LW and Zou, W and Xu, M and Kao, SJ},
title = {Thiamphenicol residues promote dark ammonia assimilation over oxidation in up-midstream of Jiulong River estuarine waters.},
journal = {Marine environmental research},
volume = {223},
number = {},
pages = {108523},
doi = {10.1016/j.marenvres.2026.108523},
pmid = {42976696},
issn = {1879-0291},
abstract = {Estuaries receive large amounts of pollutants, including nitrogen nutrients and antibiotics, discharged by human activities. Ammonium (NH4[+])/ammonia (NH3) is a preferred inorganic nitrogen nutrient utilized by microorganisms and an energy source for ammonia-oxidizing microorganisms. Nevertheless, the impact of residual antibiotics on NH3 transformation in estuary is not clear. So we investigated how thiamphenicol (TAP) - a ribosomal-targeting antibiotic widely used in aquaculture - alters dark NH3 transformations in the Jiulong River Estuary (JRE, <0.1% surface irradiance below 2 m), China, by combining [15]NH4[+] isotope tracing with metagenomic analysis. We found that tributaries are sources of antibiotics for JRE and single antibiotic concentration less than 0.1 μg/L, although the concentration varied with the seasons. In up-midstream dark zones, environmentally relevant TAP concentrations (0.01 μg/L) disproportionately stimulated NH3 assimilation over oxidation and the maximum stimulation was 118.6 ± 18.2% and 19.0 ± 1.1%, respectively. This made NH3 assimilation's contribution to total NH3 transformation maximally increased by 13 percentage points at upstream in winter and 15 percentage points at midstream in summer. Meanwhile, TAP had no directly significant effect on NH3 transformation in the downstream. Metagenomic analysis revealed that ammonia-oxidizing bacteria might be more sensitive to TAP exposure than ammonia-oxidizing archaea. Especially the ammonia-oxidizing bacteria community was composed of Betaproteobacteria. Our findings confirm that the hormetic effect of low-concentration antibiotics manifests in the NH3 transformation processes. The significant enhancement of NH3 assimilation by environmentally residual levels of TAP strengthens the flow of NH4[+] to particulate nitrogen throughout the estuary, thereby potentially prolonging the residence time of NH4[+] in aquatic systems. This provides a new perspective for understanding estuarine water eutrophication.},
}

@article {pmid42976950,
year = {2026},
author = {Yang, S and Jin, L and Deng, W and Xiao, H and Yao, Y and Xie, M and Xu, H and Zou, L},
title = {An integrated gut phage catalogue of nonhuman primates reveals functional adaptation to host ecology and evolutionary link to humans.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2082},
pages = {},
pmid = {42976950},
issn = {1471-2954},
support = {2024NSFSC1284//Sichuan Science and Technology Program/ ; 031-2222996053//Scientific Research Foundation from Sichuan Agricultural University/ ; },
mesh = {Animals ; *Bacteriophages/physiology/genetics ; Humans ; *Biological Evolution ; *Gastrointestinal Microbiome ; *Primates/virology ; Metagenome ; },
abstract = {Nonhuman primates (NHPs), the closest evolutionary relatives of humans, are pivotal models for biomedical and ecological research. Gut phage are recognized as critical modulators of gut microbial communities; however, comprehensive insight into gut phage of NHPs is lacking. We used gut metagenomes spanning 25 NHP species and constructed an integrated gut phage catalogue (IGPC) comprising 11 389 nonredundant phage genomes. Our results revealed that the composition and function of NHP gut phage were significantly influenced by host clade, dietary niche and lifestyle. Host clade exerted a stronger influence than dietary niche on gut phage diversity. The lifestyle of NHPs influenced gut phage diversity and altered auxiliary metabolic gene profiles for different NHP species. Comparatively, 78.5% of IGPC phages were detected in human guts, with higher prevalence in nonindustrialized human guts. crAss-like phage-the most prevalent human-associated phage-were abundant in NHP guts, while exhibiting distinct evolutionary differences from crAss-like phage of humans. These findings comprehensively characterize the gut phageome of NHPs, revealing NHP host-driven and environment-driven functional adaptations, and provide an evolutionary understanding of the gut phageome between NHPs and humans.},
}

Animals
*Bacteriophages/physiology/genetics
Humans
*Biological Evolution
*Gastrointestinal Microbiome
*Primates/virology
Metagenome

@article {pmid42976962,
year = {2026},
author = {Asemoloye, MD},
title = {Engineering rhizosphere microbial consortia for soil bioremediation: Mechanisms, field constraints, and evidence-based design.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {375},
number = {},
pages = {113566},
doi = {10.1016/j.plantsci.2026.113566},
pmid = {42976962},
issn = {1873-2259},
abstract = {Soil contamination continues to threaten ecosystem health and agricultural productivity worldwide. However, rhizosphere-mediated bioremediation has emerged as a nature-inspired, sustainable approach for mitigating these impacts. This review advocates field-scale implementation of rhizosphere microbiome engineering by exploiting interactions among plants, microorganisms, and soil. Unlike previous reviews that primarily summarize rhizosphere-mediated remediation processes, it integrates mechanistic, ecological, and engineering perspectives to identify critical barriers limiting field performance. This review synthesizes recent advances in rhizosphere microbiome engineering, with an emphasis on root-exudate manipulation, synthetic microbial communities (SynComs), biochar-assisted remediation, and multi-omics technologies. The evidence reviewed indicates that root exudates are key regulators of microbial recruitment, biofilm formation, and expression of contaminant-degrading genes, while engineered microbial consortia enhance functional complementarity and pollutant transformation. A comparative analysis of laboratory and field studies reveals substantial performance gaps, with highly efficient degradation observed under controlled conditions often declining following field deployment because of microbial competition, environmental variability, and contaminant sorption dynamics. The review further shows that integration of SynComs with biochar carriers and precision root-exudate engineering can improve microbial establishment and remediation efficiency. Advances in metagenomics, metabolomics, and systems biology are enabling more predictive design and monitoring of rhizosphere processes. Collectively, this review provides a mechanistic synthesis, identifies key translational bottlenecks, and outlines practical directions for developing scalable rhizosphere-based remediation technologies.},
}

@article {pmid42977125,
year = {2026},
author = {Ji, J and Du, J and Hu, F and Wu, G and Liu, L and Wang, L and Shen, B and Wei, X},
title = {Facilitating efficient anammox bacteria enrichment with loofah sponge: coupled roles of physical retention, slow-release carbon supply, and metabolic synergy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136191},
doi = {10.1016/j.biortech.2026.136191},
pmid = {42977125},
issn = {1873-2976},
abstract = {Anaerobic ammonium oxidation (anammox) provides an energy-efficient and sustainable strategy for nitrogen removal. However, the slow growth and challenging enrichment of anaerobic ammonium-oxidizing bacteria (AnAOB) remain key constraints on its engineering application. In this study, the biodegradable biomass material loofah sponge was introduced into the system to enrich AnAOB from nitrification-denitrification sludge and achieve a rapid commencement of the anammox process. During the AnAOB maturation period, the system achieved TIN (Total Inorganic Nitrogen) and NH4[+]-N removal efficiencies of 66.8% and 99.6%, respectively. Extracellular polymeric substance (EPS) analysis indicated that biofilms formed on the loofah sponge exhibited a high protein-to-polysaccharide (PN/PS) ratio, thereby enhancing microbial aggregation and facilitating AnAOB enrichment. Analysis of the microbial community structure showed that the relative abundance of the key anammox genus Candidatus Brocadia in the loofah sponge significantly increased from 0.03% in the seed sludge to 17.07%. Metagenomic analysis detected genes associated with cellulose and hemicellulose degradation, while the effluent COD profile supported gradual loofah sponge biodegradation and soluble organic matter transformation. The loofah sponge also exhibited higher abundances of genes related to central carbon metabolism, the Wood-Ljungdahl pathway, and heme biosynthesis, indicating greater metabolic potential. Overall, AnAOB enrichment on loofah sponge may have resulted from the combined effects of physical biomass retention, gradual biodegradation, and associated microbial interactions. This study offers a feasible pathway for integrating agricultural waste valorization with low-carbon nitrogen removal and steers the anammox process toward greater economic and environmental sustainability.},
}

@article {pmid42977128,
year = {2026},
author = {Ren, S and Yuan, M and Qiu, S and Jing, B and Fu, M and Jiang, Z and Deng, F},
title = {Tourmaline enhances nitrogen removal efficiency in partial Nitrification/Anammox systems via an adsorption Enrichment-Gene Regulation-Electron transfer triple mechanism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136147},
doi = {10.1016/j.biortech.2026.136147},
pmid = {42977128},
issn = {1873-2976},
abstract = {The partial nitrification (PN) / anaerobic ammonium oxidation (anammox) coupled process offers distinct advantages, including reduced aeration energy consumption and elimination of organic carbon dependence. Nevertheless, its full-scale application faces several critical challenges, particularly the difficulty in sustaining a stable nitrite accumulation rate (NAR) during the PN stage, coupled with the inherently long doubling time of anaerobic ammonium oxidation bacteria (AnAOB) in the anammox stage. Natural tourmaline (Tur), a mineral distinguished by its unique physicochemical characteristics and potential for microbial regulation, provides a promising approach to overcoming these limitations. Experimental results indicated that Tur promoted the enrichment of functional microorganisms (e.g., Nitrosomonas) and the nitrogen removal efficiency (NRE) of the PN/Anammox_Tur system showed a relative increase of 14.77%. Density functional theory (DFT) calculations further demonstrated that the active sites on Tur surfaces exhibited selective adsorption affinity for key substrates-namely NH4[+], NO2[-], and O2-thereby providing a theoretical foundation for Tur-enhanced NRE in PN/Anammox system. Analysis of microbial community structure revealed that Tur induced a significant restructuring of the microbial consortium. Moreover, metagenomic analysis confirmed the directional reconstruction of metabolic gene networks and pathways, and elucidated the differential regulation of electron transport chains by Tur via its micro-electric field. This study proposed and refined a novel mechanistic framework-termed the "Adsorption Enrichment-Gene Regulation-Electron Transfer" triple mechanism-through which Tur enhances the NRE of the PN/Anammox system. These findings provide a theoretical basis for applying natural mineral materials, particularly tourmaline, advancing mineral-based materials for biological nitrogen removal and enhancing their engineering-scale implementation feasibility.},
}

@article {pmid42977138,
year = {2026},
author = {Yang, J and Wang, R and Hu, N and Li, B and Li, Y and Xu, J and Deng, Y and Li, Y and Li, X},
title = {Polyethylene microplastics reduce aluminum uptake but obstruct nodulation in broad bean under acidic aluminum stress.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129471},
doi = {10.1016/j.envpol.2026.129471},
pmid = {42977138},
issn = {1873-6424},
abstract = {Soil acidification and microplastic pollution increasingly threaten agricultural systems worldwide, yet their combined effects on crops remain largely unexplored. In this study, we subjected broad bean (Vicia faba L.) to polyethylene (PE) microplastics, aluminum (Al) stress, or their combination, and integrated physiological assays, root metabolomics, and rhizosphere metagenomics to dissect their interactive effects. PE microplastics unexpectedly lowered root Al accumulation by 41.7% compared to Al alone, which was associated with reduced exchangeable Al in the rhizosphere. Despite this reduction, the combined PE and Al treatment still significantly suppressed root (by 50.1%) and shoot (by 42.0%) biomasses and severely compromised nodulation and nitrogen (N) acquisition, with effects similar to or even stronger than those of the mono Al treatment. Metabolomic profiling revealed that combined stress extensively downregulated ten flavonoids and fundamentally rewired flavonoid-rhizobia correlation networks, shifting potential symbiotic signaling away from compatible interactions. Metagenomic analysis further showed that while combined stress increased microbial co-occurrence network connectivity by 54.8%, it simultaneously suppressed the abundance of functional genes related to metal resistance and N cycling, pointing to a systemic metabolic burden rather than a targeted stress response. These results demonstrate that PE microplastics modulate Al bioavailability but do not mitigate phytotoxicity; instead, they exacerbate symbiotic disruption through flavonoid signaling interference and microbiome functional decline. These findings highlight the vulnerability of legume-rhizobia symbiosis to multi-stressor environments and call for a reassessment of soil management practices in regions where acidification and microplastic contamination co-occur.},
}

@article {pmid42977397,
year = {2026},
author = {Lei, W and Liu, Z and Wang, R and Liu, W and Chen, C and Zhang, S and Zhou, P and Shan, Y and Ding, S},
title = {Salinity-mediated osmotic stress reshapes the characteristic sulfur-containing aroma of spontaneously fermented Raphanus sativus L. via remodeling of lactic acid bacterial sulfur metabolism.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 5},
pages = {120887},
doi = {10.1016/j.foodres.2026.120887},
pmid = {42977397},
issn = {1873-7145},
mesh = {*Raphanus/microbiology/chemistry/metabolism ; *Fermentation ; *Osmotic Pressure ; *Sulfur/metabolism ; *Lactobacillales/metabolism ; *Odorants/analysis ; *Fermented Foods/microbiology/analysis ; *Salinity ; Metabolomics ; Sulfur Compounds ; Taste ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Low-salt fermentation has become an inevitable trend in the fermented vegetable industry, but indiscriminate salt reduction in fermented radish disrupts microecological balance, causing flavor loss and putrid off-odors. This study employed quantitative descriptive analysis (QDA), GC × GC-TOF-MS, untargeted metabolomics, and metagenomics to investigate the molecular mechanisms by which salinity-mediated osmotic changes drive flavor evolution. The results demonstrated that appropriate osmotic stress constituted a critical ecological selective pressure, which not only conferred desirable sensory attributes to the radish (pronounced jiang aroma with suppressed off-odors) but also effectively suppressed the proliferation of inorganic sulfur-producing spoilage bacteria and drove the enrichment of a co-dominant lactic acid bacteria (LAB) consortium, primarily Weissella cibaria and Leuconostoc mesenteroides. GC × GC-TOF-MS analysis revealed the key material basis underlying the aforementioned sensory changes, namely, the substantial degradation of pungent irritants (ITCs) and the dynamic retention of characteristic sulfur-containing aromas such as dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). Importantly, multi-omics analysis further elucidated the intrinsic biochemical mechanisms governing the evolution of sulfur-containing flavor in fermented radish. During the initial stage of fermentation, hyperosmotic conditions and tissue disruption triggered the extensive release of endogenous pungent substances. In response to this environmental stress, the dominant LAB not only effectively neutralized the pungency of ITCs by upregulating glutathione reduction-related genes (e.g., K00383) but also efficiently converted sulfur-containing precursors via CS lyases (K01739, K14155), thereby channeling metabolic flux toward the compensatory biosynthesis and maintenance of characteristic volatile sulfides such as DMDS and DMTS. By decoding the molecular mechanisms of pungency dissipation and sulfur aroma biosynthesis during the fermentation, this study provides new perspectives and a scientific foundation for targeted flavor optimization in low-salt fermented vegetables.},
}

*Raphanus/microbiology/chemistry/metabolism
*Fermentation
*Osmotic Pressure
*Sulfur/metabolism
*Lactobacillales/metabolism
*Odorants/analysis
*Fermented Foods/microbiology/analysis
*Salinity
Metabolomics
Sulfur Compounds
Taste
Gas Chromatography-Mass Spectrometry

@article {pmid42977442,
year = {2026},
author = {Li, Z and Li, B and Sun, X and Cao, Y and Peng, K and Shoaib, M and Yang, B and Wang, J and Ma, Y and Wang, Z and Bai, L and Li, R},
title = {Metagenomics reveals potential risks of antibiotic and metal resistance genes in agricultural production systems.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 5},
pages = {120990},
doi = {10.1016/j.foodres.2026.120990},
pmid = {42977442},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Agriculture ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Metagenome ; *Metals ; Microbiota/genetics ; Vegetables/microbiology ; Agricultural Irrigation ; },
abstract = {Agricultural environments harbor diverse microbiomes and serve as key reservoirs of resistance genes, yet their influence on fresh produce remains unclear. In this study, metagenomics was employed to reveal the microbiome and resistome in soil, irrigation water, and fresh produce surfaces in production settings. The results revealed that soil harbored the greatest microbial diversity along with the highest abundance and diversity of antibiotic resistance genes (ARGs). Fresh produce harbored diverse ARGs of potential relevance to food-chain resistance surveillance. Among the 528 bacterial metagenome-assembled genomes (MAGs) retained for genome-resolved analysis, Pseudomonadota were the predominant carriers of ARGs, including those conferring resistance to tetracyclines, aminoglycosides, and β-lactams. Interestingly, similar contigs containing rep22_1b and tet(L) were found in MAGs obtained from irrigation water and vegetable samples, indicating a high level of conservation in the genetic environment. In addition, irrigation water harbored the most abundant mobile genetic elements (MGEs), found to be significantly associated with ARG profiles. Copper (Cu) resistance genes were predominant among the detected metal resistance genes (MRGs), indicating widespread genetic potential for copper resistance across the sampled agricultural environments. Overall, these findings reveal distinct but interconnected resistome profiles across soil, irrigation water, and fresh produce and identify resistance-associated genetic features of potential relevance to food safety surveillance.},
}

*Metagenomics/methods
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
*Agriculture
*Drug Resistance, Bacterial/genetics
*Genes, Bacterial
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
Metagenome
*Metals
Microbiota/genetics
Vegetables/microbiology
Agricultural Irrigation

@article {pmid42978014,
year = {2026},
author = {Park, K and Lee, J and Hyun, D and Kim, SG and Kim, J and Hilbe, M and Gu, SH and Lim, BK and Kadjo, B and Ohdachi, SD and Truong, T and Truong, N and Palacios, G and Yanagihara, R and Song, JW},
title = {Detection and whole-genome characterisation of Regana virus in the bicoloured shrew (Crocidura leucodon) from Graubünden, Switzerland.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {42978014},
issn = {1348-8945},
support = {RS-2026-25593026//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; },
abstract = {BACKGROUND: Orthonairoviruses are of medical and veterinary importance, but the genetic diversity and geographic distribution of shrew-associated orthonairoviruses remain unclear. Shrews are increasingly recognised as hosts for diverse orthonairoviruses, including Regana virus (REGV), which has been reported in the bicoloured white-toothed shrew (Crocidura leucodon) in Germany and the Czech Republic.

METHODS: We examined archived shrew specimens collected in Graubünden Canton, Switzerland, between 2005 and 2006 using nested reverse transcription-polymerase chain reaction, metagenomic next-generation sequencing, phylogenetic analysis, pairwise sequence comparison, and protein feature annotation.

RESULTS: Nairoviral RNA was detected in three C. leucodon from Luzein and Malans, whereas four Sorex araneus and one Neomys anomalus tested negative. Complete or near-complete REGV genome sequences were recovered from the three positive animals. Swiss REGV variants clustered with REGV from Germany and the Czech Republic across the S, M, and L segments. RdRp amino acid identities were 98.8-98.9% among Swiss variants and 92.1-95.6% between REGV Np12 and German or Czech variants. Comparative protein analyses identified conserved viral ovarian tumour protease catalytic residues, similar glycoprotein precursor organisations, and nairovirus-like nucleoprotein motifs.

CONCLUSIONS: These findings document REGV in C. leucodon in Switzerland and expand the known geographical and genetic ranges of REGV in European shrew populations.},
}

@article {pmid42978029,
year = {2026},
author = {Zhang, Z and Yang, F and Zhang, Z and Liu, F and Zhuang, M and Li, J},
title = {Metagenomics reveals biogeography and functional potential of phage communities in bee gut.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42978029},
issn = {2524-4671},
abstract = {BACKGROUND: Bacteriophages (phages) are pivotal regulators of microbiome ecology and function, yet their distribution, diversity and ecological roles within the bee gut remain largely unexplored, particularly across diverse bee species and geographic regions. Here, we used a large-scale metagenomic dataset to investigate phage communities associated with seven bee species across China.

RESULTS: We recovered 121 viral operational taxonomic units (vOTUs) from 132 bee gut metagenomes, revealing that bee gut phages are dominated by the class Caudoviricetes and include numerous previously uncharacterized viral lineages. Biogeographic analyses revealed spatial structuring of phage communities such as latitudinal diversity gradient, distance-decay relationship. Variation partitioning analysis (VPA) indicated that bee host identity explained a substantially larger proportion of community variation than environmental factors. More, functional annotation further revealed that bee gut phages encode diverse carbohydrate-active enzymes (CAZymes) potentially involved in polysaccharide metabolism, as well as multiple anti-defense systems targeting bacterial antiviral mechanisms.

CONCLUSIONS: Our study demonstrates that bee gut phages exhibit biogeographic structuring and host specificity. In addition, phages carry diverse functional genes that may influence bacterial metabolism and host-microbe interactions. These findings provide a comprehensive framework for understanding the ecological roles of phages in the bee gut and highlight their importance in shaping tripartite interactions among phages, bacteria, and bee hosts.},
}

@article {pmid42978372,
year = {2026},
author = {Chi, Y and Wu, S and Lin, F and Fan, T and Liu, H and Yang, H},
title = {Reprogramming Native Cryptic Plasmids Enables Antibiotic-Selection-Free Urate Degradation by Escherichia coli Nissle 1917.},
journal = {Microbial biotechnology},
volume = {19},
number = {11},
pages = {},
pmid = {42978372},
issn = {1751-7915},
support = {XDB0810000//Chinese Academy of Sciences/ ; Z241100007724009//Beijing Municipal Science & Technology Project/ ; },
mesh = {*Uric Acid/metabolism ; Animals ; *Escherichia coli/genetics/metabolism ; *Plasmids/genetics/metabolism ; Urate Oxidase/genetics/metabolism ; Hyperuricemia/therapy ; Mice ; Truncated Hemoglobins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Hyperuricemia is associated with renal injury and disturbances in gut microbial ecology. Intestinal urate clearance by engineered probiotics is limited by antibiotic-free functional maintenance and the oxygen requirement of urate oxidase (UOX). We reprogrammed the native cryptic plasmids of Escherichia coli Nissle 1917 (EcN) to construct M12U, a marker-free dual-plasmid strain. pMUT2 carried an HucR-regulated urate-responsive UOX module, while pMUT1 encoded a low-oxygen-responsive UOX module and Tat-targeted Vitreoscilla haemoglobin (tat-VHB). M12U degraded urate in vitro and retained activity under low-oxygen conditions. In hyperuricemic mice (n = 5 per group), oral M12U reduced serum urate, creatinine, blood urea nitrogen, inflammatory cytokines and renal histopathological injury. 16S rRNA profiling showed increased microbial richness and a partial shift in community composition toward healthy controls. Shotgun metagenomics revealed enrichment of Lactobacillus johnsonii and Bacteroides acidifaciens, together with increased metabolic potential related to the pentose phosphate pathway and glutathione metabolism. Faecal metabolomics showed reduced uric acid abundance and increased thiamine monophosphate and argininosuccinic acid. These results support further evaluation of dual-native-plasmid architectures for gut-directed urate clearance.},
}

*Uric Acid/metabolism
Animals
*Escherichia coli/genetics/metabolism
*Plasmids/genetics/metabolism
Urate Oxidase/genetics/metabolism
Hyperuricemia/therapy
Mice
Truncated Hemoglobins/genetics/metabolism
Bacterial Proteins/genetics/metabolism

@article {pmid42978454,
year = {2026},
author = {Zhang, L and Han, D},
title = {Metagenomic next-generation sequencing as an adjunctive diagnostic tool for Clonorchis sinensis infection: a case report.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/17460913.2026.2755565},
pmid = {42978454},
issn = {1746-0921},
abstract = {Clonorchis sinensis is a foodborne liver fluke. This case highlights acute cholangitis in a non-endemic area, where raw-fish history was initially absent and identified only after multidisciplinary team (MDT) discussion. Conventional tests were negative. A 53-year-old female had fever, epigastric pain, leukopenia, elevated C-reactive protein (CRP) and liver enzymes, and progressive eosinophilia (6.3% to 19.7%). Abdominal computed tomography (CT) and magnetic resonance cholangiopancreatography (MRCP) showed cholangitis. Plasma and stool metagenomic next-generation sequencing (mNGS) detected C. sinensis (4 and 3375 reads), prompting stool microscopy that confirmed characteristic eggs. This complementary strategy enabled timely praziquantel, with resolution of fever and abdominal pain, declining eosinophilia, and improved liver function. She was discharged on day 16 and asymptomatic at 30-day follow-up. Clonorchiasis should be considered in eosinophilic cholangitis even in non-endemic areas; mNGS is a valuable complementary tool when conventional tests fail and presentations are atypical.},
}

@article {pmid42978490,
year = {2026},
author = {Sheng, Y and Dai, X and Lu, J and Zhang, H and Cai, P},
title = {The Potential Role of Gut Microbiome Dysbiosis and Functional Reprogramming in Colorectal Liver Metastasis via the Gut-Liver Axis.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {11},
pages = {},
pmid = {42978490},
issn = {2573-8348},
support = {2024KY1551//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2025KY1386//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2025KY1503//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2024Z229//Science and Technology Innovation Yongjiang 2035 Key Research and Development Project of Ningbo/ ; 2022E50008//Zhejiang Provincial Clinical Research Center for CANCER/ ; 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; },
mesh = {Humans ; *Liver Neoplasms/secondary/microbiology ; *Colorectal Neoplasms/pathology/microbiology ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Feces/microbiology ; Middle Aged ; Aged ; Liver/pathology/microbiology ; Case-Control Studies ; Metagenomics ; Biomarkers, Tumor ; },
abstract = {BACKGROUND: Colorectal liver metastasis (CRLM) is a leading cause of mortality in colorectal cancer (CRC), yet current surveillance often misses occult micrometastases, underscoring an urgent need for early non-invasive biomarkers and mechanistic insights.

AIMS: This study aimed to investigate gut microbiota dysbiosis and functional alterations associated with CRLM and explore potential non-invasive biomarkers.

METHODS AND RESULTS: Fecal metagenomic sequencing was performed in 60 participants, comprising healthy controls, patients with non-metastatic CRC, and patients with synchronous CRLM (n = 20 per group). Microbial composition, functional pathways, co-occurrence networks, and clinical associations were systematically analyzed, and a random forest model was constructed to identify potential diagnostic biomarkers. Results showed that gut microbiota dysbiosis intensified as CRC progressed toward CRLM, characterized by the depletion of commensal flora and significant enrichment of specific genera, such as Eikenella and Porphyromonas. Functionally, the gut microbiome displayed stage-specific remodeling, shifting from infection- and virulence-related pathways in CRC to functions associated with microbial secondary metabolism and stress adaptation in CRLM. Furthermore, SPIEC-EASI-based network analysis revealed a sparser and more compartmentalized microbial ecological structure in CRLM, with [Clostridium] symbiosum, Campylobacter concisus, and Coprococcus eutactus emerging as module hubs. A random forest model integrating nine core taxa and one virulence factor (VF0160 FeoAB) achieved an overall 97.5% classification accuracy in discriminating CRLM from non-metastatic CRC, indicating the potential of fecal metagenomic biomarkers for future risk stratification. However, prospective validation in larger multicenter cohorts is required before clinical translational utility.

CONCLUSION: Collectively, our findings suggest that gut microbiota dysbiosis and functional reprogramming are strongly associated with CRLM progression, potentially through remodeling the hepatic pre-metastatic niche via the gut-liver axis.},
}

Humans
*Liver Neoplasms/secondary/microbiology
*Colorectal Neoplasms/pathology/microbiology
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome
Male
Female
Feces/microbiology
Middle Aged
Aged
Liver/pathology/microbiology
Case-Control Studies
Metagenomics
Biomarkers, Tumor

@article {pmid42978728,
year = {2026},
author = {Liu, H and Feng, S and Tang, M and Sun, J and Tian, R and Zhang, S},
title = {Berberine improves lipid levels, vascular function, and gut microbial-dependent metabolites in stable coronary artery disease patients.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1945710},
pmid = {42978728},
issn = {2296-861X},
abstract = {Berberine (BBR) has been demonstrated to exert cardiovascular protective effects by regulating lipids and ameliorating inflammation. Recent studies reported the interaction between BBR and gut microbiota in various metabolic diseases due to its low bioavailability. However, few studies examine the effect of BBR on the gut microbiota in coronary artery disease (CAD) individuals. We hence conducted a parallel-controlled, regularly visited clinical trial with 23 stable CAD patients who recently underwent percutaneous coronary intervention and completed a 12-week BBR ± standard therapy treatment. The BBR intervention was associated with a directional improvement in endothelial function, enhanced levels of low-density lipoprotein cholesterol (LDL-C), and a reduction in circulating inflammatory mediators (IL-1α, IL-17, MCP-1, MIP-1β, and VEGF). Using metagenomics and metabolomic studies, we identified that bacterial signatures varied significantly with gradually increasing doses of BBR. These results showed that a specific group of short-chain fatty acid (SCFA)-producing bacteria, mainly Ruminococcus sp., Roseburia sp., and Anaerostipes hadrus, were elevated following the BBR intervention, which was also negatively correlated with inflammatory factors. Notably, regardless of the background standard therapy, BBR reshaped gut-microbiota-encoded aromatic amino acid catabolism: it selectively enriched the microbial L-dopa, 3-hydroxyphenylacetic acid, and phenylpropionic acid branches, which were anchored by increased abundances of dopamine β-monooxygenase, porA, and acdA genes. Overall, we investigated the role of BBR in regulating microbial metabolic alterations and vascular function. Targeted restoration of the gut microbiota may present a novel ecological approach for managing cardiovascular disease.},
}

@article {pmid42978829,
year = {2026},
author = {Ding, X and Bao, P and Huang, X and Xu, R and Tang, X and Wu, Y and Cui, X and Lu, Y},
title = {Predicting clinically actionable metagenomic next-generation sequencing in sepsis through dynamic inflammatory trajectories.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1949602},
pmid = {42978829},
issn = {1664-302X},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) improves pathogen detection in sepsis, but positive results do not always prompt antimicrobial modification. We investigated whether dynamic host-response trajectories during the mNGS peri-report interval could predict clinical actionability.

METHODS: This retrospective single-center study included 109 adults with sepsis who underwent mNGS and conventional culture, and 72 patients with complete prespecified predictor data entered model development. Baseline and dynamic logistic models were assessed for discrimination, calibration, prediction error, and exploratory decision-curve performance. Final fixed models underwent 1,000-resample bootstrap optimism correction.

RESULTS: mNGS positivity was 94.8% in the actionable group and 84.3% in the non-actionable group, with broader descriptive pathogen detection than culture. In the complete-case cohort, the peri-report change in white blood cell count (dWBC) remained associated with actionability after adjustment for the included baseline variables (adjusted OR, 1.14; 95% CI, 1.02-1.28; P = 0.025). Apparent AUC increased from 0.744 to 0.816 after adding dWBC. Optimism-corrected AUCs were 0.697 and 0.768, and corrected Brier scores were 0.228 and 0.207. No baseline-WBC interaction was detected (P = 0.494).

CONCLUSION: A less pronounced decline or an increase in WBC from pre-mNGS sampling to post-report reassessment was associated with a greater likelihood of subsequent documented mNGS-related antimicrobial modification.},
}

@article {pmid42979227,
year = {2026},
author = {Betancurt-Anzola, D and Vanegas, J and Jurgensen, SK and Wrighton, KC and Santamaría-Vanegas, J and Couradeau, E},
title = {Genome-resolved metagenomics reveals nonmethanogenic soil lineages in an Andean páramo wetland.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag294},
pmid = {42979227},
issn = {2730-6151},
abstract = {Wetlands are the largest natural source of atmospheric methane, and tropical wetlands are projected to drive the greatest increase in emissions under climate change, yet high-altitude tropical systems remain largely absent from global frameworks predicting this response. Here, we investigated soil metagenomes from the páramo ecosystem in Chingaza National Natural Park, Colombia, across three ecosites. Microbial community composition differed significantly among ecosites, with peatland soils exhibiting the highest diversity. Genome-resolved metagenomics recovered 109 high-quality metagenome-assembled genomes (MAGs); 8.3% (9 MAGs) could not be assigned to any described genus, representing phylogenetically novel lineages, while 37.6% (41 MAGs) were absent from the wetland-specific MUCC database but present in GTDB. Functional analyses revealed widespread Wood-Ljungdahl pathway potential, complemented by the bacterial reductive glycine pathway and reverse tricarboxylic acid cycle. No methanogenesis marker (mcrABG) was detected in any high- or medium-quality genomes or assembled contigs, identifying the genomically resolved community as nonmethanogenic. A read-level search nonetheless recovered a low-abundance methanogen signal concentrated in peatland and affiliated with hydrogenotrophic lineages typical of acidic peatlands, indicating that methanogenesis is present but minor. Metabolic potential instead supported acetogenic carbon fixation and sulfate reduction, suggesting a carbon-cycling regime distinct from canonical methane-dominated wetlands. Together, these findings establish tropical alpine páramos as overlooked reservoirs of phylogenetically novel microbial diversity with metabolic potential distinct from other wetlands. Public release of these MAGs expands genomic representation of tropical alpine ecosystems and provides a foundation for improving predictions of carbon cycling in high-altitude ecosystems.},
}

@article {pmid42979256,
year = {2026},
author = {Chen, J and Duan, F and Zhu, G and Liu, H and Wang, X and Cui, Y and Luo, Y and Zhang, H},
title = {Multi-omics in coronary atherosclerosis: mechanistic insights and advances in precision diagnosis and treatment.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1974206},
pmid = {42979256},
issn = {1664-2392},
mesh = {Humans ; *Multiomics ; *Coronary Artery Disease/diagnosis/therapy/metabolism/genetics ; *Precision Medicine/methods ; Metabolomics/methods ; Genomics/methods ; Biomarkers/metabolism ; Proteomics/methods ; },
abstract = {Coronary atherosclerosis, driven by the interplay of lipid metabolic derangements and chronic inflammation, constitutes the pathological basis of atherosclerotic cardiovascular disease and has emerged as the leading cause of mortality among Chinese residents. In patients with acute coronary syndrome, subsequent events may arise from initially nonculprit coronary lesions that appear angiographically mild. Invasive coronary angiography, the conventional diagnostic reference standard, is inherently invasive and incapable of characterizing plaque biological properties. Meanwhile, traditional risk factors only enable crude risk stratification, resulting in a critical shortage of precise early clinical screening modalities. Multi-omics technologies enable comprehensive molecular profiling of the human organism and effectively address the limitations of conventional detection approaches. Nevertheless, existing investigations remain largely confined to single-omics analyses; candidate biomarkers lack validation in large independent cohorts, and substantial bottlenecks persist in clinical translation. This review evaluates the respective advantages and limitations of genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and gut metagenomics in coronary atherosclerosis research. It elucidates the scientific value of integrated multi-omics analysis in dissecting pathogenic regulatory networks, unraveling gut-heart axis mechanisms, and identifying targets for precision therapy. Furthermore, it summarizes cutting-edge technological advances including single-cell multi-omics, spatial multi-omics, liquid biopsy, and AI-powered multi-omics integration, and compiles multi-omics risk prediction models developed on the basis of large-scale population cohorts. By bridging genetic susceptibility, cellular remodeling, peripheral molecular signatures, and plaque phenotypes, multi-omics integration can underpin early risk warning for high-risk populations, plaque subtyping, and therapeutic efficacy monitoring. Looking ahead, the establishment of standardized, multicenter prospective cohorts and the application of Mendelian randomization to infer causal relationships will be pivotal. These efforts are essential to translate multi-omics into a practical framework for comprehensive precision medicine across the entire continuum of coronary atherosclerosis.},
}

Humans
*Multiomics
*Coronary Artery Disease/diagnosis/therapy/metabolism/genetics
*Precision Medicine/methods
Metabolomics/methods
Genomics/methods
Biomarkers/metabolism
Proteomics/methods

@article {pmid42979304,
year = {2026},
author = {Li, X and Gao, Y and Zhang, Z and Zhang, Y and Cao, W and Deng, W and Wang, S and Wei, X and Gao, Z and Yao, L and Wang, S and Xie, Y and Li, M},
title = {Metagenomic study in a predominantly adult cohort with hepatitis of unknown etiology.},
journal = {Biosafety and health},
volume = {8},
number = {5},
pages = {359-367},
pmid = {42979304},
issn = {2590-0536},
abstract = {Hepatitis of unknown origin (HUO) remains a diagnostic challenge, with metagenomic studies underexplored in adult cohorts. This study characterized the plasma and fecal virome in a predominantly adult HUO cohort (48 adults and 1 adolescent). A total of 59 samples (44 plasma, 15 fecal) from 49 patients were subjected to ultra-multiplex targeted ribonucleic acid (RNA) sequencing (139 RNA viruses) and unbiased metagenomic sequencing. Targeted sequencing detected HCV in one plasma sample, confirmed by follow-up reverse transcription-polymerase chain reaction (RT-PCR) and seroconversion, leading to case reclassification. Metagenomic sequencing identified HBV sequences in another patient, along with sporadic goose circovirus (GoCV) and an unconfirmed low-level influenza A-like signal. Viral community analysis revealed distinct niche-specific profiles between plasma and feces. Overall, this exploratory study failed to identify a common pathogenic agent, underscoring the etiological heterogeneity of HUO. The detection of known hepatotropic viruses highlights the diagnostic value of metagenomic sequencing in complementing conventional serology and reclassifying some HUO cases. Larger controlled studies are warranted.},
}

@article {pmid42979446,
year = {2026},
author = {Sekikawa, Y and Horiba, K and Hashino, M and Soneda, K and Kato, T},
title = {Infective endocarditis due to a novel Gemella species revealed by metagenomic sequencing.},
journal = {ASM case reports},
volume = {2},
number = {6},
pages = {},
pmid = {42979446},
issn = {2996-2684},
abstract = {BACKGROUND: Gemella species are rare causes of infective endocarditis, and accurate species identification can be challenging with routine diagnostic methods. We report infective endocarditis caused by a novel Gemella species, highlighting the diagnostic value of sequencing-based approaches for bacteria not registered in public databases and the risk of misclassification when novel species are not represented in reference databases.

CASE SUMMARY: A 55-year-old Japanese man presented with fatigue, anorexia, and altered mental status. Echocardiography revealed vegetations on the mitral and tricuspid valves with severe mitral regurgitation, and imaging demonstrated multiple systemic embolic events. Blood cultures grew gram-positive cocci that were initially identified as Gemella bergeri by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The patient received antimicrobial therapy and underwent mitral valve replacement and tricuspid valve repair. Culture of the excised valve tissue was negative. Metagenomic sequencing of the valve vegetation detected a Gemella species distinct from G. bergeri. Genome assembly from sequencing data showed 94.5% average nucleotide identity with a reference G. bergeri genome, supporting classification as a novel species. Whole-genome sequencing of the blood culture isolate demonstrated near-complete concordance with the organism detected in the valve tissue. The patient recovered with a 6-week course of intravenous penicillin G after blood cultures became sterile.

CONCLUSION: This case demonstrates that rare Gemella infections may be misidentified by routine mass spectrometry. It underscores the importance of sequencing-based methods for accurate pathogen identification and highlights a diagnostic pitfall associated with database-dependent identification in infective endocarditis.},
}

@article {pmid42979661,
year = {2026},
author = {Li, G and Dong, S and Liu, C and Yan, H and Yang, J and Rensen, PCN and Shi, B and Wang, Y},
title = {Dietary butyrate alleviates high-fat diet-induced colonic mucosal impairment accompanied by increased gut-derived indole-3-acetic acid and enhanced PPARγ signaling.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1971187},
pmid = {42979661},
issn = {1664-2392},
mesh = {Animals ; Male ; Mice ; *Diet, High-Fat/adverse effects ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Humans ; *Colon/metabolism/drug effects/pathology ; *PPAR gamma/metabolism ; Gastrointestinal Microbiome/drug effects ; *Indoleacetic Acids/metabolism ; Signal Transduction/drug effects ; *Butyric Acid/pharmacology ; Caco-2 Cells ; Intestinal Barrier Function ; *Butyrates/pharmacology ; },
abstract = {INTRODUCTION: High-fat diet (HFD) induces intestinal barrier impairment, associated with gut microbiota dysbiosis, endotoxin translocation and metabolic dysfunction. Dietary butyrate has been reported to improve intestinal homeostasis, but the underlying mechanism remains incompletely understood. This study aimed to investigate the effects of dietary butyrate on HFD-induced colonic mucosal dysfunction and to explore underlying mechanisms with respect to the role of gut microbiota and its metabolites.

METHODS: Male APOE*3-Leiden.CETP mice, a well-established translational model for diet-induced metabolic dysfunction, were fed an HFD with or without 5% sodium butyrate. Metabolic phenotypes, plasma lipopolysaccharide (LPS), colonic histology, inflammatory responses, and tight junction-associated changes were assessed. Fecal microbiota transplantation (FMT) was performed in antibiotic-treated recipient mice to assess the contribution and transferability of butyrate-shaped gut microbiota. Cecal metagenomic sequencing and LC/MS-based colonic indole-3-acetic acid (IAA) measurement were performed. Caco-2 cells were used to assess the direct effects of sodium butyrate and IAA on enterocytes and to determine, through pioglitazone treatment and PPARγ knockdown, whether PPARγ mediates IAA-induced enterocyte responses.

RESULTS: Dietary butyrate induced favorable changes in multiple colonic barrier-associated parameters, including improved colonic architecture, lower circulating LPS levels, decreased Tnf-a and Il-1b expression, and increased CLDN2, Reg-family, and PPARγ expression in the colon. In addition, butyrate reduced body weight gain, fat mass accumulation and improved glucose metabolism. FMT from butyrate-treated donors partially reproduced these beneficial effects in HFD-fed recipients. Metagenomic analysis showed enrichment of Bacteroidota and Bacteroides, particularly B. uniformis and B. thetaiotaomicron, accompanied by increased colonic IAA levels. In Caco-2 cells, IAA increased the expression of PPARγ, Reg4, and CLDN2. While PPARγ agonist pioglitazone mimicked the upregulation of REG4 and CLDN2 expression by IAA, siRNA-induced PPARγ knockdown attenuated IAA-induced REG4 and CLDN2 upregulation.

CONCLUSION: Dietary butyrate improves colonic mucosal homeostasis under HFD feeding, accompanied by gut microbial remodeling and increased colonic IAA levels. Together with the PPARγ-dependent epithelial response to IAA observed in Caco-2 cells, these findings suggest a potential mechanistic framework linking butyrate-associated microbial changes, IAA metabolism, and epithelial PPARγ signaling.},
}

Animals
Male
Mice
*Diet, High-Fat/adverse effects
*Intestinal Mucosa/metabolism/drug effects/pathology
Humans
*Colon/metabolism/drug effects/pathology
*PPAR gamma/metabolism
Gastrointestinal Microbiome/drug effects
*Indoleacetic Acids/metabolism
Signal Transduction/drug effects
*Butyric Acid/pharmacology
Caco-2 Cells
Intestinal Barrier Function
*Butyrates/pharmacology

@article {pmid42980271,
year = {2026},
author = {Li, J and Zhou, W and Cai, L and Shen, H and Lu, H and Fan, J},
title = {Metagenomic Next-Generation Sequencing of Mycoplasma hominis Infection in an Immunocompromised Patient: A Case Report.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {237},
pages = {},
doi = {10.3791/72450},
pmid = {42980271},
issn = {1940-087X},
mesh = {Humans ; *Mycoplasma hominis/genetics/isolation & purification ; *Mycoplasma Infections/microbiology/immunology ; *Immunocompromised Host ; Middle Aged ; Male ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Mycoplasma hominis is an underrecognized opportunistic pathogen that can cause extra-genitourinary infections, particularly in immunocompromised hosts. This case report describes a persistent soft tissue infection following a wooden splinter injury in a 52-year-old immunocompromised man, in whom M. hominis was identified by blood mNGS after conventional microbiological investigations were inconclusive. The patient developed recurrent fever, wound pain, swelling, and exudation. Empirical treatment with ertapenem and subsequent surgical intervention did not provide sustained clinical improvement, while conventional microbiological investigations remained inconclusive. Peripheral blood was therefore analyzed by mNGS, which detected M. hominis, human betaherpesvirus 5, and GB virus C. For M. hominis, nine species-specific reads were identified, with a relative abundance of 21.5% for the genus Mycoplasma and 99% confidence for species-level identification. The mNGS finding was interpreted together with the refractory clinical course and the absence of a convincing alternative bacterial pathogen. Following further surgical management and multidisciplinary evaluation, targeted antimicrobial therapy with intravenous moxifloxacin plus omadacycline was administered, followed by oral omadacycline after discharge. The patient subsequently became afebrile, pain improved, and inflammatory markers progressively declined. This case demonstrates the potential utility of blood mNGS for identifying an atypical pathogen in an immunocompromised patient with culture-negative, treatment-refractory infection. The findings also emphasize that low-read mNGS results should be interpreted in conjunction with clinical findings, conventional microbiological investigations, and treatment response.},
}

Humans
*Mycoplasma hominis/genetics/isolation & purification
*Mycoplasma Infections/microbiology/immunology
*Immunocompromised Host
Middle Aged
Male
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods

@article {pmid42980350,
year = {2026},
author = {Yuan, L and Anantharaman, K and Ma, B and Camargo, AP and Chen, L},
title = {Scaffold-level validation is needed for phage-host inference from metagenome-assembled genomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag276},
pmid = {42980350},
issn = {1751-7370},
abstract = {Accurate phage-host prediction underpins ecological interpretation and experimental validation of uncultivated phages, yet most current approaches rely heavily on metagenome-assembled genomes (MAGs). This reliance implicitly assumes that MAG-level quality metrics, such as completeness and contamination, ensure scaffold-level correctness. Here, we demonstrate that this assumption can be violated under particular challenging conditions. Tetranucleotide frequency (TNF) analyses reveal that CRISPR-associated regions often diverge compositionally from their host genomes, increasing the risk of misbinning, while experimentally validated phage-host genome pairs show consistent TNF separation between phages and their hosts, challenging compositional binning assumptions. Through controlled simulations, we further show that the incorporation of substantial amounts of TNF-matched, non-host phage sequences into high-quality MAGs does not substantially alter standard completeness and contamination estimates, rendering such errors largely undetectable. Together, these results expose a systematic and underappreciated source of bias in MAG-based phage-host inference and highlight the need for explicit scaffold-level validation beyond conventional genome-quality metrics. We further propose a practical scaffold-level validation framework that integrates structural linkage and taxonomic consistency to improve the reliability of phage-host inference from MAGs.},
}

@article {pmid42980424,
year = {2026},
author = {Sun, S and Guo, M and Zhou, Y and Deng, F and Wang, H and Wei, D},
title = {Identification and Engineering of an l-Threonine Aldolase from Agrobacterium pusense for Efficient l-Serine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {43},
pages = {34116-34125},
doi = {10.1021/acs.jafc.6c07415},
pmid = {42980424},
issn = {1520-5118},
support = {24HC2810400//Science and Technology Commission of Shanghai Municipality/ ; },
mesh = {*Serine/biosynthesis ; *Glycine Hydroxymethyltransferase/genetics/metabolism/chemistry ; *Agrobacterium/enzymology/genetics/chemistry ; *Bacterial Proteins/metabolism/genetics/chemistry ; Protein Engineering ; Kinetics ; Substrate Specificity ; Biocatalysis ; Molecular Dynamics Simulation ; },
abstract = {l-Serine is a high-value amino acid, but enzymatic production is limited by insufficient catalytic activity and limited formaldehyde tolerance. A metagenomic library derived from glufosinate-exposed soil was mined to identify an l-threonine aldolase from Agrobacterium pusense (ApLTA). The substrate tunnel and active pocket were engineered through tunnel analysis, structural comparison, consensus design, and residue plasticity-guided polarity scanning. The resulting quadruple mutant D88M/T202S/A57S/F234M (Mut4) exhibited 48.5-fold higher catalytic efficiency than wild-type ApLTA. At 1 M formaldehyde loading, Mut4 increased l-serine concentration from 23.0 to 87.3 g L-1, with a space-time yield of 21.8 g L-1 h-1, the highest reported for LTA-catalyzed l-serine synthesis. Mut4 also showed enhanced activity toward multiple aromatic aldehydes. Molecular dynamics simulations further revealed the molecular basis for its enhanced catalytic efficiency. This study provides the first demonstration of highly efficient l-serine synthesis using an engineered LTA and offers a new strategy for enzymatic l-serine production.},
}

*Serine/biosynthesis
*Glycine Hydroxymethyltransferase/genetics/metabolism/chemistry
*Agrobacterium/enzymology/genetics/chemistry
*Bacterial Proteins/metabolism/genetics/chemistry
Protein Engineering
Kinetics
Substrate Specificity
Biocatalysis
Molecular Dynamics Simulation

@article {pmid42980489,
year = {2026},
author = {Xu, L and Liang, P and Wang, Y and Zhang, X-J and Chai, L-J and Xu, H-Y and Wang, S-T and Zhang, S-Y and Shen, C-H and Lu, Z-M and Huang, WE and Xu, Z-H},
title = {Monitoring single-cell metabolic phenotyping changes of Daqu microbiota during fermentation by Raman spectroscopy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0161226},
doi = {10.1128/aem.01612-26},
pmid = {42980489},
issn = {1098-5336},
abstract = {Monitoring microbial community dynamics during natural food fermentation is essential for stabilizing fermentation processes and improving product flavor profiles. This study employed single-cell Raman spectroscopy to monitor the metabolic change of Daqu microbiota during fermentation. First, we developed an operational phenotypic unit (OPU)-based clustering method to process Raman spectral data of a nine-member microbial community. The clustering was validated by sorting out representative single cells from different OPUs and performing 16S/ITS region sequencing. Second, single-cell Raman spectroscopy was applied to the mixed Daqu sample throughout fermentation, identifying 10 OPUs and 54 sub-OPUs. Single cells from different OPUs were sorted and sequenced to obtain taxonomic annotation, which were correlated with the Raman spectral characteristics of each OPU. The OPU-based Raman spectroscopy method was successfully used to monitor the single-cell metabolic phenotypes of Daqu microbiota during fermentation, and taxonomic annotations revealed the succession of microbial community structure. This study presents a novel approach for monitoring the dynamics of metabolic phenotypes within Daqu microbial communities, offering a data-driven decision-making approach for subsequent production operations in multi-species fermentation processes.IMPORTANCEMicrobial communities play pivotal roles in diverse industrial processes, yet monitoring their metabolic dynamics remains challenging. Current omics approaches, including metagenomics, transcriptomics, and mass spectrometry-based metabolomics, fail to establish direct genotype-phenotype linkages at the single-cell level and often require destructive sampling. This study introduces operational phenotypic units (OPUs) as a novel framework to bridge this gap by integrating single-cell Raman spectroscopy with sequencing technologies. Our method enables non-destructive, rapid monitoring of metabolic phenotypes while preserving cells for downstream analysis. By applying this approach to solid-state Daqu fermentation, we demonstrate its capability to track microbial community succession and identify functionally distinct populations in real time. This data-driven strategy offers significant potential for optimizing multi-species fermentation processes across food, environmental, and biotechnological industries, providing a powerful tool for microbial community management and process control.},
}

@article {pmid42980911,
year = {2026},
author = {Wang, L and ZHao, J and Huang, H and Yu, X and Xu, W},
title = {Effect of continuous application of pig manure on soil antibiotic resistance genes.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42980911},
issn = {1618-1905},
support = {CARS-23-B08//China Agriculture Research System/ ; 32272801//National Natural Science Foundation of China/ ; },
abstract = {The large-scale application of livestock and poultry manure in protected agriculture is common; however, research on the spread of antibiotic resistance genes (ARGs) from this practice remains limited. Herein, 16 S and metagenomic sequencing methods were used to investigate the effects of eight consecutive years of pig manure application on tetracycline (TC) antibiotics in protected soil and to evaluate the ecological consequences. In addition, the characteristics of soil ARGs and bacterial diversity were explored, and the potential hosts of ARGs in protected soil and the influence of environmental factors on these potential hosts and ARGs were preliminarily investigated. After 8 years of applying composted pig manure, the total tetracycline residues in the protected soil was as follows: commercial organic fertilizer soil > pig manure soil > rapeseed cake fertilizer soil. Soil enzymes indirectly affect ARG abundance by influencing the microbial community structure. g__unclassified_p__Acidobacteria and g__unclassified_c__Actinomycetia may be the two most important ARG hosts, with a highly significant positive correlation with 32 ARG subtypes. Total nitrogen (TN) and soil organic matter (SOM) significantly promoted the abundance of these two important potential hosts. Nocardioides, g__unclassified_o__Solirubrobacterales, Actinoplanes, and Methyloceanibacter are potential hosts for intI1. TC, Soil urease(S-UE), Soil acid phosphatase(ACP), Soil β-glucosidase(S-β-GC), TN, total phosphorus (TP), and SOM significantly promoted the abundance of potential intI1 hosts. Soil environmental factors collectively accounted for 72.27% of ARG variation, making them the most important factor affecting ARGs. Our research will support manure management in protected agriculture to reduce ARG spread.},
}

@article {pmid42623301,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {86},
number = {21},
pages = {5374-5390},
pmid = {42623301},
issn = {1538-7445},
support = {P30 CA125123/CA/NCI NIH HHS/United States ; R01 CA282786/CA/NCI NIH HHS/United States ; R21 CA218732/CA/NCI NIH HHS/United States ; R37 CA237384/CA/NCI NIH HHS/United States ; 1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
mesh = {Animals ; Humans ; *Pancreatic Neoplasms/metabolism/pathology/microbiology/therapy ; Mice ; Tumor Microenvironment ; *Carcinoma, Pancreatic Ductal/metabolism/pathology/microbiology/therapy ; Cancer-Associated Fibroblasts/metabolism/pathology ; Interleukin-6/metabolism ; *Microbiota ; *Exercise/physiology ; Stromal Cells/metabolism/pathology ; Actins/metabolism ; Male ; Female ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer-associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

Animals
Humans
*Pancreatic Neoplasms/metabolism/pathology/microbiology/therapy
Mice
Tumor Microenvironment
*Carcinoma, Pancreatic Ductal/metabolism/pathology/microbiology/therapy
Cancer-Associated Fibroblasts/metabolism/pathology
Interleukin-6/metabolism
*Microbiota
*Exercise/physiology
Stromal Cells/metabolism/pathology
Actins/metabolism
Male
Female

@article {pmid42969355,
year = {2026},
author = {Pusz-Bochenska, K and Murugesan, K and Senchyna, F and Lalljie, A and Budvytiene, I and Banaei, N},
title = {Accuracy of plasma cell-free DNA PCR versus mNGS for non-invasive diagnosis of invasive mold disease.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0117526},
doi = {10.1128/jcm.01175-26},
pmid = {42969355},
issn = {1098-660X},
abstract = {UNLABELLED: Cell-free DNA (cfDNA) detection in plasma is a novel testing modality for non-invasive diagnosis of invasive mold disease (IMD) in immunocompromised patients. The accuracy of PCR compared to metagenomic next-generation sequencing (mNGS) for diagnosis of IMD remains unknown. Plasma samples from patients with proven and probable IMD and no IMD were tested with mold PCR and shotgun mNGS. Mold PCR detected Aspergillus species, Mucorales agents, Fusarium species, Scedosporium species, and Lomentospora prolificans. The sensitivity and specificity of mold PCR and mNGS were measured. Ninety-four patients with proven (48) and probable (48) IMD due to Aspergillus species (64), Mucorales agents (13), Scedosporium species and Lomentospora prolificans (13), and Fusarium species (6), and 62 patients with no IMD were included in this study. 99.4% (155) of the patients were immunosuppressed. The overall sensitivity and specificity were 62.5% (60/96; 95% CI 52.0-72.2) and 99.8% (535/536; 95% CI 99.0-100), respectively, for mold PCR and 43.8% (42/96; 95% CI 33.6-54.3; P < 0.001) and 99.6% (534/536; 95% CI 98.7-100; P = 1.0), respectively, for mNGS. The proportion of mold PCR-positive mNGS-negative results was 16.0% (4/25) in focal cases compared with 25.0% (11/44; P = 0.384) and 18.5% (5/27; P = 0.810) in multifocal and disseminated cases, respectively. The median PCR cycle threshold was 40.6 (IQR, 37.5-41.5) in PCR-positive mNGS-negative cases compared with 37.3 (IQR, 34.5-39.3; P = 0.004) in PCR-positive mNGS-positive cases. Plasma cfDNA PCR is more sensitive than mNGS for the diagnosis of IMD in immunocompromised patients. Lower sensitivity of mNGS was associated with lower mold cfDNA burden.

IMPORTANCE: Invasive mold disease (IMD) is a major cause of morbidity and mortality in immunocompromised patients. Early diagnosis and initiation of tailored antifungal therapy are critical for optimizing outcomes in patients with IMD. Detection of circulating fungal cell-free DNA (cfDNA) in the acellular fraction of blood is a novel testing modality that is increasingly used for early and non-invasive diagnosis of IMD. This study represents the first head-to-head accuracy study to compare the sensitivity and specificity of PCR with mNGS for the diagnosis of IMD. The study showed that the overall mold PCR was significantly more sensitive compared with mNGS, while both assays demonstrated very high specificity. Similar trends were observed in a smaller subgroup of patients with invasive aspergillosis, mucormycosis, and scedosporiosis. The findings have implications for assay selection when seeking to non-invasively diagnose IMD in immunocompromised patients.},
}

@article {pmid42969359,
year = {2026},
author = {Vestergaard, SZ and Liu, L and Dueholm, MKD and Nielsen, PH},
title = {Genome-resolved taxonomy, global distribution, and EPS potential of Zoogloea, the canonical floc-former in wastewater treatment systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0102426},
doi = {10.1128/msystems.01024-26},
pmid = {42969359},
issn = {2379-5077},
abstract = {The bacterial genus Zoogloea is the fourth most abundant genus in wastewater treatment plants (WWTPs) globally, where it plays key roles in floc formation and nutrient removal but can also contribute to viscous bulking when highly abundant. The taxonomic assignment of Zoogloea has historically been inconsistent, as several taxa were classified based on phenotypic characteristics and later reassigned to other families or orders. This has obscured both the identity and distribution of Zoogloea and hindered interpretation of its floc-forming mechanisms, which have been attributed to polysaccharides that may not originate from phylogenetically defined Zoogloea. Using our collection of more than 22,000 high-quality genomes from global activated sludge systems (MiDAS global genome catalog), we identified 47 genomes affiliated with the phylogenetically defined Zoogloea. In combination with abundance data, this enabled resolution of the genus' taxonomy, biogeographical distribution, and metabolic diversity. Building on this framework, we mapped the phylogenetic distribution of a recently identified Zoogloea-associated floc-forming polysaccharide biosynthesis gene cluster by screening the MiDAS global genome catalog and GTDB. The gene cluster was identified across multiple genera within the Burkholderiales order, including Zoogloea, Thauera, Azoarcus, and Ca. Accumulibacter, as well as several previously undescribed taxa. The gene cluster is broadly conserved, with minor variations in gene composition and synteny, suggesting corresponding differences in polysaccharide structure. Genomes encoding this cluster also consistently contained co-occurring floc-regulating genes, indicating a common and widespread mechanism underlying floc formation in activated sludge systems.IMPORTANCEOperation of activated sludge systems depends on stable microbial floc formation for the separation of biomass from treated effluent. Floc formation is mediated by extracellular polymeric substances (EPS) produced by microorganisms, yet the identity, distribution, and biosynthesis of these polymers remain poorly characterized. Zoogloea is widely regarded as a canonical and model floc-forming genus associated with EPS production in wastewater treatment systems. However, its taxonomic classification has historically been problematic, as organisms were often assigned to Zoogloea based on morphology, leading to widespread misclassifications. This has blurred the true origin of polysaccharides attributed to the genus as well as their wider phylogenetic distribution, which has not been systematically resolved. Here, we map the distribution of the Zoogloea-associated polysaccharide biosynthesis gene cluster across a global genome data set, providing a framework to link phylogenetically defined taxa with floc-forming potential. This improves our understanding of EPS production in activated sludge systems and may support strategies for enhanced resource recovery.},
}

@article {pmid42970519,
year = {2026},
author = {Naumova, OY and Dobrynin, PV and Litwin, G and Rychkov, SY and Milham, MP and Grigorenko, EL},
title = {Salivary microbiome, socioeconomic status, and cognitive performance: Triangulating the relationship.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0361602},
pmid = {42970519},
issn = {1932-6203},
mesh = {Humans ; *Microbiota ; Child ; *Cognition/physiology ; *Social Class ; Adolescent ; Female ; Male ; *Saliva/microbiology ; Black or African American ; Hispanic or Latino ; Wechsler Scales ; Socioeconomic Disparities in Health ; },
abstract = {Research increasingly demonstrates that endogenous bacterial communities (microbiomes) are associated with both cognitive functioning and socioeconomic status (SES). In this study, we used a metagenomics approach to characterize oral microbiome diversity in Hispanic and African American children aged 6-16 years. We examined how microbiome composition and SES were related to cognitive performance, as assessed by the Wechsler Intelligence Scale for Children (WISC). Our findings indicate that SES and the microbiome contributed complementary, comparably sized influences on cognitive functioning. Together, variability in conventional SES indicators and microbiome composition accounted for approximately 10% of the variability in WISC scores. These results highlight the importance of integrating both social and biological determinants of health when studying cognitive performance and other psychological outcomes.},
}

Humans
*Microbiota
Child
*Cognition/physiology
*Social Class
Adolescent
Female
Male
*Saliva/microbiology
Black or African American
Hispanic or Latino
Wechsler Scales
Socioeconomic Disparities in Health

@article {pmid42970552,
year = {2026},
author = {Zhu, H and Lin, X and Wang, R and Zhang, T and Xu, W and Gao, W and Fang, F and Huang, J and Sun, Y},
title = {Metagenomic and metabolomic analysis of a bryozoan-associated microbial complex from the Hanjiang River, China.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0358304},
pmid = {42970552},
issn = {1932-6203},
mesh = {Animals ; *Bryozoa/microbiology/metabolism/genetics ; China ; *Rivers/microbiology ; *Metabolomics/methods ; *Metagenomics/methods ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Bryozoans are ancient colonial animals that have existed for over 470 million years and are widely distributed across aquatic environments. Recently, many spherical colloids (average diameter≈1 meter in diameter), containing bryozoans and diverse microorganisms, were found in the Hanjiang river in China. In this study, we investigated these bryozoan-dominated microbial complexes using metagenomic sequencing, metabolomic profiling, and complementary approaches.

RESULTS: The results revealed that the microbial structure dominated by bryozoans included eukaryotes such as fungi, microalgae, as well as prokaryotes such as bacteria, and acellular entities such as viruses. All members form a highly integrated consortium that collaboratively maintains community function and stability, which displayed the shape and structure of a regular microbial complex and increased in size. Additionally, the results suggested the predominately presence of Proteobacteria were particularly abundant and are known to produce bryozoans in response to bryozoan signals. Interesting, it was implied that a decrease or even a loss in virulence occurs when pathogenic microorganisms become members of the complex. This is the first study focusing on the composition and metabolites of the unusual microorganism complex. The results discovered the close and intriguing connections within the microbial communities dominated by the ancient organism bryozoan through multi-omics technologies. It showed that both eukaryotes and prokaryotes can coordinate, thereby forming a stable composite structure.},
}

Animals
*Bryozoa/microbiology/metabolism/genetics
China
*Rivers/microbiology
*Metabolomics/methods
*Metagenomics/methods
Bacteria/genetics/metabolism

@article {pmid42970847,
year = {2026},
author = {Hu, Y and Hu, J and Yuan, H and Liu, F and Li, C and Xu, J and Yin, S},
title = {Impaired intestinal riboflavin transport induces systemic and medullary metabolic remodeling accompanied by gut microbiota alterations.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {67},
number = {},
pages = {106837},
doi = {10.1016/j.clnu.2026.106837},
pmid = {42970847},
issn = {1532-1983},
abstract = {BACKGROUND: Riboflavin is an essential micronutrient required for cellular energy metabolism and redox homeostasis. Although intestinal riboflavin absorption is critical for maintaining systemic flavin homeostasis, the metabolic consequences of impaired riboflavin transport and its associations with gut microbiota alterations remain poorly understood.

METHODS: Intestinal epithelial-specific Slc52a3 conditional knockout (cKO) mice were generated using a Cre-loxP strategy. Integrated multi-omics analyses, including fecal metagenomics, serum metabolomics, and medulla oblongata metabolomics, were performed to characterize microbial and metabolic alterations associated with impaired riboflavin absorption. Targeted LC-MS/MS analysis of medullary flavins, inflammatory mediator profiling, and reactive oxygen species (ROS) fluorescence staining were performed to further characterize the medullary phenotype.

RESULTS: Intestinal Slc52a3 deletion markedly reduced riboflavin levels in serum and medulla, with targeted LC-MS/MS confirming decreased medullary riboflavin and FAD levels. Serum metabolomics suggested alterations in tryptophan-related metabolites, including serotonin, indoleacetaldehyde, 5-hydroxytryptophan, and l-formylkynurenine. Medullary metabolomics suggested lipid-associated metabolic alterations, including arachidonic acid-related pathways, accompanied by increased inflammatory mediators and ROS levels. Metagenomic analyses revealed altered gut microbial composition without significant changes in alpha diversity or predicted riboflavin biosynthetic potential. Exploratory correlation analyses revealed associations between selected microbial taxa and circulating tryptophan-related and medullary lipid metabolites.

CONCLUSIONS: Impaired intestinal riboflavin transport induces systemic and medullary metabolic remodeling accompanied by gut microbiota alterations. These findings highlight the importance of intestinal SLC52A3 in maintaining flavin homeostasis and provide insights into its associations with host metabolic alterations and gut microbial composition.},
}

@article {pmid42971202,
year = {2026},
author = {Poyet, M and Rühlemann, M and Schaan, AP and Ma, Y and Moitinho-Silva, L and Wacker, EM and Jebens, H and Patel, L and Nguyen, LTT and Zimmer, A and Plichta, D and McDonald, D and Stevens, C and Agyei, A and Afihene, MY and Asibey, SO and Awuku, YA and Badiane, AS and Corzett, C and Deme, A and Dominguez-Rodrigo, M and Duah, A and Fezeu, A and Froment, A and Gibbons, S and Girard, C and Hooker, J and Ibrahim, F and Iqaluk, D and Juimo, V and Kettunen, P and Lafosse, S and Lango-Yaya, E and Lee, SC and Lehtimäki, J and Lim, YAL and Mabulla, A and Mahachai, V and Mohamed, RS and Moniz, K and Mwikarago, IE and Nartey, YA and Ndiaye, D and Noel, M and Onyekwere, C and Pin, TM and Plymoth, A and Roberts, L and Ruokolainen, L and Rusine, J and Segurel, L and Shapiro, BJ and Sigwazi, S and Sistiaga, A and Valles, K and Vatanen, T and Vilaichone, RK and Rosenstiel, P and Baines, J and Franke, A and Ellinghaus, D and Knight, R and Daly, M and Xavier, RJ and Alm, EJ and Groussin, M},
title = {Industrialization drives convergent microbiome and host physiological shifts in the human metaorganism.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.10.016},
pmid = {42971202},
issn = {1097-4172},
abstract = {Understanding how industrialization reshapes the human metaorganism requires integrating microbiome ecology with host physiology across globally diverse populations. Here, we generate multivariate data from the Global Microbiome Conservancy cohort, including gut microbiome, immunoglobulin A (IgA) sequencing, host genotyping, diet, lifestyle, and fecal biomarker profiles, to investigate host-microbiome interactions across gradients of industrialization and geography. We show that industrialization is associated with homogenized microbial compositions, reduced microbial diversity, and lower community stability, independent of host confounders. We further show that industrialization is linked to elevated markers of gut stress, increased IgA secretion, and altered patterns of IgA-bacteria interactions. Finally, we show that microbiome-based disease predictors trained on industrialized populations are uninformative in less industrialized cohorts, highlighting limited cross-population transferability. Together, our results reveal coordinated restructuring of the microbial ecosystem and host physiology and emphasize the need for inclusive, globally representative data to improve translational microbiome applications across diverse human populations.},
}

@article {pmid42971204,
year = {2026},
author = {Rühlemann, M and Ma, Y and Szánthó, LL and Waschina, S and Moitinho-Silva, L and Mews, LC and Faus-Camarena, J and Jebens, H and Costa, J and Juimo, V and Fezeu, A and Agyei, A and Afihene, MY and Asibey, SO and Awuku, YA and Duah, A and Nartey, YA and Ibrahim, F and Lim, YAL and Tan, MP and Onyekwere, C and Rusine, J and Mwikarago, IE and Baines, J and Franke, A and Szöllősi, GJ and Xavier, RJ and Alm, EJ and Groussin, M and Poyet, M},
title = {Convergent genomic evolution of human gut bacteria along an industrialization gradient.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.10.014},
pmid = {42971204},
issn = {1097-4172},
abstract = {Whether human-associated environments drive adaptive genome evolution in gut commensal bacteria remains largely unknown. Here, we investigate how genomic adaptation in gut bacteria differs between industrialized and non-industrialized human populations. We generated a collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that, compared with metagenome-assembled genomes (MAGs), paired isolate genomes recover more functional elements and signals of horizontal gene transfer (HGT). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent HGT events. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as the stress response, cell-envelope remodeling, and central metabolism. Our results demonstrate that industrialization drives convergent genome evolution in gut bacteria, providing a framework for understanding the mechanisms of microbial adaptation to rapidly changing human environments.},
}

@article {pmid42971424,
year = {2026},
author = {Wang, Z and Xu, X and Shang, S and Fu, Y and Wang, J and Ren, Y and Jin, Z and Yue, G and Guo, Y and Yuan, X and Zhang, Q and Li, S and He, N},
title = {Host-microbiome asynchronous decoupling reveals systemic metabolic allostatic overload mediated by gut genomic potential degradation.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {156817},
doi = {10.1016/j.metabol.2026.156817},
pmid = {42971424},
issn = {1532-8600},
abstract = {BACKGROUND & AIMS: Metagenomic aging clocks predict chronological age but lose explanatory power during midlife (35-65 years). We hypothesized that cumulative allostatic load drives microenvironmental alterations, leading to asynchronous decoupling of metagenomic and metabolomic profiles.

METHODS: A metagenomic clock was trained on a lifespan cohort (N = 4551) and evaluated in a midlife sub-cohort (N = 1868). Independent metagenomic (N = 843) and fecal metabolomic (N = 106) cohorts assessed functional and phenotypic trajectories. Within a paired multi-omics cohort (N = 99), Procrustes and spatial dispersion analyses quantified topological decoupling. Metabolic biological age gap (metBAG) and metabolome-wide association studies (MWAS) characterized allostatic load signatures.

RESULTS: The lifespan model achieved R[2] = 0.444 (MAE = 13.09 years). In midlife, model fit decreased (R[2] = 0.187), whereas MAE narrowed to 6.73 years, indicating greater phenotypic stability. Concurrently, core taxa (e.g., Bifidobacterium breve) exhibited age-related declines. Paired analysis revealed significant spatial decoupling; microbial dispersion exceeded metabolic dispersion, suggesting host metabolic remodeling buffers microbial divergence. Elevated metBAG correlated with clinical parameters. Under high allostatic load, 1,3,7-trimethyluric acid enrichment and all-trans retinoic acid depletion were associated with the systemic aging transition.

CONCLUSIONS: We identified an asynchronous decoupling during midlife: basal microbial decline precedes systemic aging and is initially buffered by host metabolic remodeling. When allostatic load exceeds compensatory capacity, specific metabolite enrichment may accelerate systemic aging. This framework facilitates sub-health quantification and informs microbiome-targeted interventions.},
}

@article {pmid42971484,
year = {2026},
author = {Zhao, L and Zhang, Y and Tian, T and Huang, Y and Gu, Y and He, X and Tang, J and He, S},
title = {Sulfur-iron-driven autotrophic constructed wetlands for coupled nitrogen removal and phosphorus transformation under low carbon-to-nitrogen ratio conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136170},
doi = {10.1016/j.biortech.2026.136170},
pmid = {42971484},
issn = {1873-2976},
abstract = {Constructed wetlands are widely used for nitrogen removal, yet their performance in low carbon-to-nitrogen (C/N) wastewater is often constrained by insufficient electron donors. Autotrophic denitrification provides a carbon-independent alternative, but systems relying on single inorganic substrates frequently exhibit limited electron supply and unstable nutrient transformation. Here, a sulfur-iron-slag-based constructed wetland (SCW) was developed to investigate nitrogen removal and its linkage with phosphorus dynamics under progressively decreasing C/N conditions. The system achieved consistently high nitrate removal (>93%) and a maximum total nitrogen removal efficiency of 79.22%, substantially outperforming a conventional sand-based wetland (53.58%) at a C/N ratio of 0.67. Enhanced nitrogen removal was associated with the sulfur-iron functional medium and sustained autotrophic denitrification. However, phosphorus showed a contrasting response: although aqueous P release decreased with continued operation, the SCW remained a net aqueous P source throughout the reported period, accompanied by redistribution of solid-phase P toward Fe/Al-associated and Ca-associated fractions. Microbial and metagenomic analyses revealed the enrichment of sulfur-oxidizing and autotrophic denitrifying taxa together with shifts in nitrogen- and sulfur-related functional-gene profiles, consistent with enhanced sulfur-associated autotrophic potential. Functional gene profiles further indicated that electron transfer processes governed the integration of multi-element biogeochemical cycles rather than isolated increases in individual pathways. Overall, this study elucidates process-level coupling between enhanced autotrophic nitrogen removal and dynamic phosphorus transformation, providing mechanistic insights and practical guidance for optimizing constructed wetlands treating low-C/N wastewater.},
}

@article {pmid42971485,
year = {2026},
author = {Si, T and Chen, X and Wang, S and Bian, R and Liu, X and Zhang, X and Joseph, S and Mao, Y and Li, L and Pan, G},
title = {Biochar-mediated N-Fe redox coupling for Cd immobilization and N2O mitigation in flooded paddy soil.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136185},
doi = {10.1016/j.biortech.2026.136185},
pmid = {42971485},
issn = {1873-2976},
abstract = {Coupled soil N and Fe redox processes influence heavy-metal mobility and greenhouse-gas emissions. As an electron shuttle, biochar can directly mediate N and Fe redox transformations. However, how this function regulates electron allocation within N-Fe redox processes and whether this regulation contributes to Cd immobilization and N2O mitigation remains unclear. Here, anaerobic incubation experiments combined with electrochemical characterization, electron allocation analysis and metagenomic analysis were conducted in Cd-contaminated paddy soils. Nitrate addition suppressed Fe(III) reduction and amorphous Fe oxide formation in the control treatments, indicating competition between nitrate and Fe(III) reduction. In contrast, biochar increased Fe(III) and nitrate reduction rates by 18-402% and 53-258%, respectively. Biochar also enhanced soil electron-transfer rate and capacity, enriched electroactive microorganisms and extracellular electron-transfer functional genes. The electron allocation analysis showed that biochar increased total quantified electron consumption and suggested that biochar may alleviate competition between nitrate and Fe(III) reduction. Enhanced Fe(III) reduction increased Fe(II) production and may have promoted nitrate-associated Fe(II) oxidation, with amorphous Fe oxide contents increasing by 9-63%. These Fe transformations redistributed Cd into Fe/Mn oxide-bound fractions and decreased CaCl2-extractable Cd by 29-55%. Within the nitrate reduction pathways, biochar increased absolute electron consumption by dissimilatory nitrate reduction to ammonium (DNRA), while decreasing that by denitrification. These changes were accompanied by 10-49% higher NH4[+] concentrations and 13-19% lower cumulative N2O emissions. These findings highlight the role of biochar-mediated electron transfer in regulating electron allocation within coupled N-Fe redox processes, providing novel insights into concurrent Cd immobilization and N2O mitigation in paddy soils.},
}

@article {pmid42971771,
year = {2026},
author = {Murthy, SSN and Chuan, J and Jiang, Y and Chen, W and Beiko, RG and Li, X},
title = {Seasonal and Environmental Influences on Microbial Community Dynamics in the Dunk River Watershed, Prince Edward Island, Canada.},
journal = {Environmental microbiology},
volume = {28},
number = {11},
pages = {},
pmid = {42971771},
issn = {1462-2920},
support = {//Canadian Food Inspection Agency/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Dalhousie University/ ; },
mesh = {*Rivers/microbiology/chemistry ; Seasons ; *Microbiota ; Prince Edward Island ; *Bacteria/classification/isolation & purification/genetics ; Ecosystem ; Metagenomics ; },
abstract = {Riverine ecosystems are crucial biogeochemical hubs, with their microbial communities playing a key role in nutrient cycling and overall ecosystem health. This study used shotgun metagenomic sequencing to characterize the seasonal and environmental drivers of taxonomic and functional microbial community structure (read depth between 1.91 and 30.44 bp) in four tributaries of the Dunk River watershed in Prince Edward Island (PEI), a landscape shaped by intensive agriculture and groundwater-dominated streamflow, where the seasonal and land-use impacts on the river's microbiome remain understudied. Although taxonomic composition showed no significant spatial variation among sampling sites, functional profiling identified subtle but distinct spatial signatures, primarily driven at the site with the least human impacts. Mass effects driven by above- or below-ground water dispersal pathways may override local selective pressures, resulting in a more uniform community structure across different locations. The study also identified significant correlations between certain rare microbial taxa and nutrient concentrations. This work provides critical baseline data on microbial ecology in PEI river systems, indicating that while temporal factors are the primary identifiable drivers among the measured variables, a substantial majority of the community variance remains unexplained, likely reflecting the inherent stochasticity of open riverine ecosystems.},
}

*Rivers/microbiology/chemistry
Seasons
*Microbiota
Prince Edward Island
*Bacteria/classification/isolation & purification/genetics
Ecosystem
Metagenomics

@article {pmid42972085,
year = {2026},
author = {Persinoti, GF and Martins, MP and Silva, CBC and Streit, RSA and Paixão, DAA and Martins, GH and Higasi, PMR and Braatz, GM and Silva, MKP and Morão, LG and Martins-Junior, J and Stoffel, F and Ciol, H and Noske, GD and Miyamoto, RY and Oliveira, GM and Martim, DB and Oliveira, CHM and Almeida, OAC and Araújo, EA and Andrade, MO and Santos, CA and Wolf, LD and Souza, AR and Gonçalves, FAC and de Mello, DMD and Morais, MAB and Porto, J and Lombard, V and Giuseppe, PO and Terrapon, N and Lemos, LN and Henrissat, B and Carvalho, VL and da Silva, VMF and Murakami, MT},
title = {Metabolic specialization in the gut microbiome of aquatic mammalian herbivores.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42972085},
issn = {2058-5276},
support = {2021/04891-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2021/09793-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2021/09793-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2024/15257-1//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2024/05551-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2024/17771-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/09386-8//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2023/15596-8//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2024/15182-1//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 303898/2024-0//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; 304440/2024-8//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; NNF20SA0067193, NNF22OC0077058, and NNF22SA0077601//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Sirenians, such as manatees, are the only extant mammals fully adapted to aquatic herbivory. Through specialized hindgut fermentation, they play a role in modulating nutrient fluxes and carbon cycling across tropical coastal and riverine ecosystems. However, our understanding of their gut microbiome and its metabolic potential remains elusive. Here we present an ultradeep genomic atlas of the gut microbiome from 47 freshwater and marine manatees spanning distinct developmental stages, comprising 1,215 non-redundant prokaryotic metagenome-assembled genomes and their associated virome. The manatee microbiome encodes a multilayered enzymatic repertoire for plant cell wall deconstruction, including free enzymes, cellulosomes and CAZyme-enriched outer membrane vesicles, alongside diverse pathways for aromatic catabolism. Combining biochemical and structural approaches, we characterize a previously unrecognized enzymatic pathway involving epilactase, which enables a specific Bacillota species to exploit a carbohydrate inaccessible to most microbial life, defining a specialized biochemical strategy for nutrient niche partitioning. Together, these findings uncover the microbial and metabolic basis of aquatic mammalian herbivory.},
}

@article {pmid42972344,
year = {2026},
author = {Rutkowska, N and Wojtynek, J and Śliżewska, W and Nielipiński, M and Sypka, M and Kurek, Z and Łukanowska, O and Prażanowska, W and Modrzejewska, P and Lewocha, B and Horążak, W and Naporowski, I and Bednarek, W and Nielipińska, D and Drożdżyński, P and Marchut-Mikołajczyk, O},
title = {Integrating culture-dependent and culture-independent approaches to explore the diversity of endophytic bacteria associated with Urtica dioica L. in Poland with screening of pigment-producing isolates.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42972344},
issn = {1475-2859},
support = {SKN/SP/571010/2023//Ministerstwo Nauki i Szkolnictwa Wyższego, Poland/ ; SKN/SP/571010/2023//Ministerstwo Nauki i Szkolnictwa Wyższego, Poland/ ; },
mesh = {*Endophytes/isolation & purification/classification/genetics/metabolism ; *Urtica dioica/microbiology ; Poland ; *Bacteria/isolation & purification/classification/metabolism/genetics ; *Pigments, Biological/biosynthesis ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Plants can thrive in changing environmental conditions with the help of microorganisms that inhabit their tissues, known as endophytes. However, many endophytes do not grow under standard laboratory conditions, but metagenomic analysis provides insights into microbial diversity and community structure. This study aimed to compare communities of endophytic bacteria from stinging nettle (Urtica dioica L.) isolated throughout different regions of Poland, both culturable and non-culturable, and to identify shared bacterial taxa across all locations, which may represent a putative core microbiome.

RESULTS: From all regions, 66 bacterial isolates were obtained. 32% of them were identified, mostly as Bacillus and Pseudomonas members, which are common endophytes of many plants. Although a substantial proportion of reads remained unclassified, metagenomic data enabled the tentative identification of several genera present across all samples, including Acinetobacter, Bacillus, Citrobacter, Enterococcus, Escherichia, Klebsiella, Paenibacillus, Salmonella, Vibrio, and Xanthomonas. Among the isolates, Exiguobacterium sp. SP2-R3 exhibited the most intense orange pigmentation. The results indicate that the pigment is putatively quinone-like and demonstrates promising scavenging activity.

CONCLUSIONS: The study deepens our understanding of U. dioica L. endophytic communities and highlights the value of combining cultivation-based methods with metagenomic approaches. Also, among the isolates with visible potential to produce pigments, the best producer was selected and identified. It is recognized that those isolates may possess additional valuable properties that warrant deeper investigation.},
}

*Endophytes/isolation & purification/classification/genetics/metabolism
*Urtica dioica/microbiology
Poland
*Bacteria/isolation & purification/classification/metabolism/genetics
*Pigments, Biological/biosynthesis
Phylogeny
Biodiversity
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid42972434,
year = {2026},
author = {Branders, S and Grabherr, MG and Ahmad, R},
title = {Voyager: rapid taxonomic characterization of long-read mixed-species sequencing samples in sorted motif distance space.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42972434},
issn = {1474-760X},
support = {336420//Norges Forskningsråd/ ; },
mesh = {*Algorithms ; *Sequence Analysis, DNA/methods ; *Software ; Nucleotide Motifs ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; },
abstract = {Voyager is a novel algorithm that complements real-time sequencing by rapidly mapping long sequencing reads with insertion and deletion errors to a known database of organisms. It utilizes Sorted Motif Distance Space, distances between exact matches of short motifs sorted by rank, to represent sequence similarity in a highly compressed, computationally efficient manner while enabling strain-level discrimination. Voyager incorporates a deconvolution algorithm to discern closely related genomes. It achieves an average species-level accuracy of 99% across 15 datasets, outperforming all evaluated methods. Voyager maintains CPU runtimes comparable to the current fastest methods while using less than half the memory.},
}

*Algorithms
*Sequence Analysis, DNA/methods
*Software
Nucleotide Motifs
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods

@article {pmid42972501,
year = {2026},
author = {Huang, Y and Shi, J and Li, Z and Ma, Y and He, P and Yang, R and Lei, Z},
title = {Effects of castration-associated hormonal changes on rumen microbiota, metabolism, and meat quality in Holstein cattle.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42972501},
issn = {1471-2180},
support = {2026CXZX-781//Gansu Provincial Department of Education: "Innovation Star" Project/ ; 25ZDNA008//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology/metabolism ; *Rumen/microbiology/metabolism ; Male ; *Hormones/blood/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Meat/analysis ; *Orchiectomy/veterinary ; *Gastrointestinal Microbiome ; *Microbiota ; Animal Feed/analysis ; *Red Meat/analysis ; Metabolomics ; },
abstract = {BACKGROUND: It remains unclear whether hormones and microorganisms affect growth performance and meat quality, and whether there is an interaction between them. In this study, nine Holstein bulls and nine Holstein steers were fed for 270 days under the same management conditions. We combined rumen microbiomics, metabolomics, and epithelial transcriptomics with serum and muscle metabolomics as well as serum hormone detection, to explore how rumen microbes and hormones jointly regulate growth performance and beef quality of Holstein cattle.

RESULTS: Compared with bull group, the Lightness (L*), Redness (a*), Yellowness (b*), intramuscular fat and marbling score were significantly increased in steer group (P < 0.05). Serum testosterone, triiodothyronine, thyroxine, growth hormone, leptin, and glucagon levels were significantly lower in steer group, which also reflected that castration inhibited final body weight (FBW), average daily gain (ADG), dry matter intake (DMI), gain feed ratio (G/F) (P < 0.05). Cellulase, pectinase, β-glucosidase, acetate, propionate and butyrate were significantly lower, while α-amylase and lipase were significantly higher in steer group (P < 0.05). The rumen metagenome indicates unclassified_o_Bacteroidales and unclassified_f_Lachnospiraceae were significantly abundant of steer and bull groups, respectively; the functions that determined beef quality were primarily in lipid and fat anabolic pathway; and the hormones and microbes had a strong correlation. Serum and muscle metabolites of steer group were involved in fatty acid metabolism, whereas bull group were primarily involved in amino acid and protein metabolism; and Lysophosphatidylethanolamines (LPE (0:0/20:3) and (20:3/0:0)) significantly influenced marbling score and intramuscular fat. The explanations of comprehensive membership value (CMV) in the rumen microbiome, rumen metabolism, serum metabolism, muscle metabolism, and rumen epithelial genes were 29.90%, 4.50%, 10.50%, 1.60%, and 0.01%.

CONCLUSION: Castration could inhibit growth performance and improve meat quality, by mainly regulating rumen microorganisms (29.90%) and serum metabolism (10.50%); this study also provides a significant theoretical basis for analyzing the regulatory mechanisms of castration on growth performance and meat quality of cattle.},
}

Animals
Cattle/growth & development/microbiology/metabolism
*Rumen/microbiology/metabolism
Male
*Hormones/blood/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
*Meat/analysis
*Orchiectomy/veterinary
*Gastrointestinal Microbiome
*Microbiota
Animal Feed/analysis
*Red Meat/analysis
Metabolomics

@article {pmid42972591,
year = {2026},
author = {Kumari, P and N, S and Ballamoole, KK and Afrough, B and Jagadesh, A},
title = {Metagenomic next-generation sequencing for the detection of viruses from respiratory samples: a systematized review on current methods and future directions.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42972591},
issn = {1743-422X},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; *Viruses/genetics/isolation & purification/classification ; *Virus Diseases/diagnosis/virology ; Molecular Diagnostic Techniques/methods ; Sensitivity and Specificity ; Genome, Viral ; },
abstract = {The comprehensive identification of viruses using metagenomic next-generation sequencing (mNGS) has revolutionized the infectious disease diagnosis. Accurate detection of viruses on time is crucial to effectively control the outbreak. This review has meticulously analyzed the use of mNGS to identify viruses from respiratory samples, emphasizing how sample enrichment and amplification methods affect viral detection efficiency and genome coverage. A total of 66 studies were considered to evaluate sequencing workflows and their alignment with routine molecular techniques. Among these studies, the most frequently used method to enrich viruses was centrifugation (50%), followed by enzymatic treatment (45%). Sequence-independent single-primer amplification (SISPA) and switching mechanism at the 5' end of RNA template (SMART) was most commonly used amplification methods, which produced better genome coverage for most of the viruses. While mNGS showed better detection capabilities, they showed variable agreement with routine diagnostic methods, with sensitivity varying from 62.5% to 95%. Rhinovirus was detected mainly in lower respiratory tract infections (68%) and respiratory syncytial viruses in upper respiratory tract infections (60%). Although mNGS has the potential, its routine use is hampered by various technical issues. Overcoming these limitations through optimized sequencing protocols and greater cost-effectiveness will be pivotal in integrating mNGS into clinical applications.},
}

*High-Throughput Nucleotide Sequencing/methods
Humans
*Metagenomics/methods
*Respiratory Tract Infections/virology/diagnosis
*Viruses/genetics/isolation & purification/classification
*Virus Diseases/diagnosis/virology
Molecular Diagnostic Techniques/methods
Sensitivity and Specificity
Genome, Viral

@article {pmid42973481,
year = {2026},
author = {Wang, J and Hu, J and Liang, X and Yuan, F and Ren, L and Wang, T and Gao, Z and Duan, Y},
title = {Metagenomic next-generation sequencing of aqueous humor guides targeted therapy for Staphylococcus epidermidis endophthalmitis in chronic ocular graft-versus-host disease: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1966692},
pmid = {42973481},
issn = {1664-3224},
mesh = {Humans ; *Endophthalmitis/drug therapy/microbiology/diagnosis/etiology ; Male ; *Staphylococcus epidermidis/genetics ; *Aqueous Humor/microbiology ; High-Throughput Nucleotide Sequencing ; *Staphylococcal Infections/drug therapy/diagnosis/microbiology/etiology ; Adult ; Vancomycin/therapeutic use/administration & dosage ; *Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Chronic Disease ; Hematopoietic Stem Cell Transplantation/adverse effects ; },
abstract = {PURPOSE: To report a case of Staphylococcus epidermidis endophthalmitis in chronic ocular graft-versus-host disease, refractory to empirical broad-spectrum antibiotics, rapidly identified by metagenomic next-generation sequencing of aqueous humor, and successfully managed with targeted vancomycin without vitrectomy.

METHODS: Case report.

RESULTS: A 35-year-old male with chronic oGVHD following allo-HSCT for acute myeloid leukemia developed endophthalmitis after 10 months of progressive disease. Slit-lamp examination revealed central corneal ulceration (4 × 2 mm) with hypopyon (1 mm). B-scan ultrasonography confirmed mild vitreous haze. Conventional microbiological workup of aqueous humor-including Gram stain, potassium hydroxide (KOH) mount, and bacterial/fungal culture-yielded negative results. Aqueous humor mNGS detected 5,543 unique reads of S. epidermidis (genome coverage 12.3%, no co-pathogens), exceeding the clinical significance threshold. Based on this result, therapy was switched to targeted intracameral and periocular vancomycin (10 mg/ml) combined with intravenous vancomycin (0.5 g twice daily). Vancomycin was selected for its reliable Gram-positive coverage, including coagulase-negative staphylococci, referencing the established intravitreal dose of 1 mg/0.1 mL. The infection was controlled without corneal perforation or vitrectomy. AMT was performed for persistent epithelial defects. At 1.5 years follow-up, anatomical preservation was maintained (BCVA 20/400 OD; 20/40 OS).

CONCLUSION: In immunosuppressed oGVHD patients with suspected endophthalmitis, aqueous humor mNGS overcomes the diagnostic limitations of conventional culture and guides a timely switch from empirical antibiotics to targeted therapy, achieving infection control and anatomical preservation without invasive vitrectomy or enucleation.},
}

Humans
*Endophthalmitis/drug therapy/microbiology/diagnosis/etiology
Male
*Staphylococcus epidermidis/genetics
*Aqueous Humor/microbiology
High-Throughput Nucleotide Sequencing
*Staphylococcal Infections/drug therapy/diagnosis/microbiology/etiology
Adult
Vancomycin/therapeutic use/administration & dosage
*Metagenomics/methods
Anti-Bacterial Agents/therapeutic use/administration & dosage
Chronic Disease
Hematopoietic Stem Cell Transplantation/adverse effects

@article {pmid42973669,
year = {2026},
author = {Scaffidi, AD and Scaffidi, SJ and Carling, J and Fajfer, A and Ali, M and Ono, R and Hilyard, A and Buksbaum, RE and Kumar, V and Shukla, R and Mishra, S and Jain, S and Yadav, H and Heckmann, BL},
title = {Rubicon is a critical regulator of immune barrier integrity and limits enteric pathogen infection.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1889997},
pmid = {42973669},
issn = {1664-3224},
mesh = {Animals ; Intestinal Barrier Function ; Mice ; Mice, Knockout ; *Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology ; *Intestinal Mucosa/immunology/metabolism/microbiology ; *Salmonella typhimurium/immunology ; Gastrointestinal Microbiome/immunology ; *Salmonella Infections/immunology ; Mice, Inbred C57BL ; Enterobacteriaceae Infections/immunology ; },
abstract = {INTRODUCTION: Intestinal immune barrier integrity is governed by coordinated epithelial renewal, junctional organization, and vesicular trafficking. Herein, we identify a previously undefined role for the noncanonical autophagy protein Rubicon in the maintence of the intestinal immune barrier. Rubicon-dependent vesicular pathways, including conjugation of ATG8 proteins to single membranes (CASM) function to support vesicle trafficking homeostasis.

METHODS: Mice with global deletion of Rubicon (Rubcn[-]/[-]) were used to evaluate impact on gut permeability using FITC-dextran, overall intestinal anatomy and histopathology, junction protein homeostasis, and pathogen response.

RESULTS AND DISCUSSION: Loss of Rubicon led to impaired intestinal barrier function and increased intestinal permeability, supported by a 10-fold increase in circulating FITC-dextran. Rubicon-deficiency was also associated with multiple anatomical changes including elongation of the small and large intestines, shortened small-intestinal villi, epithelial hyperplasia, and lymphoid expansion, amongst others. Mechanistically, Rubicon-deficiency resulted in aberrant trafficking and mislocalization of key junctional proteins including E-cadherin and occludin. Furthermore, metagenomic analysis of the intestinal microbial community revealed broad restructuring of the intestinal microbiota compared to WT animals. Importantly, Rubicon-deficiency hypersensitized mice to enteric pathogen infection. Rubcn[-]/[-] mice exhibited accelerated and worsened mortality in addition to systemic bacteremia following infection with Salmonella Typhimurium. Bacterial burden was significantly in multiple tissues including mesenteric lymph nodes, spleen, and liver, further supporting failure of the intestinal barrier following loss of Rubicon. Collectively, these findings identify Rubicon as a novel and foundational regulator of IEC vesicular processing, epithelial junctional organization, intestinal barrier function, and host defense beyond established roles in innate immune cells.},
}

Animals
Intestinal Barrier Function
Mice
Mice, Knockout
*Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology
*Intestinal Mucosa/immunology/metabolism/microbiology
*Salmonella typhimurium/immunology
Gastrointestinal Microbiome/immunology
*Salmonella Infections/immunology
Mice, Inbred C57BL
Enterobacteriaceae Infections/immunology

@article {pmid42973731,
year = {2026},
author = {Feng, S and Liu, J and Zhang, X and Zhang, L and Zhao, S and Jiang, N and Cai, J and Zheng, Y and Gai, W and Xu, C},
title = {Metagenomic next-generation sequencing of matched donor-recipient pairs reveals pathogen transmission dynamics and informs antimicrobial therapy in liver transplantation: a retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1919428},
pmid = {42973731},
issn = {2235-2988},
mesh = {Humans ; *Liver Transplantation/adverse effects ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; *Tissue Donors ; *Transplant Recipients ; *Anti-Infective Agents/therapeutic use ; Adult ; },
abstract = {BACKGROUND: Post-transplant infections remain a leading cause of morbidity and mortality after liver transplantation (LT). Conventional microbiological culture has well-recognized limitations in sensitivity and pathogen spectrum coverage. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic platform. However, its systematic evaluation across matched donor-recipient pairs, including characterization of possible donor-to-recipient pathogen transmission and its impact on antimicrobial stewardship, remains limited.

METHODS: We retrospectively enrolled 45 consecutive LT donor-recipient pairs. Multiple sample types were collected from donors (n = 124) and recipients (n = 97) and subjected to both mNGS and conventional culture. Recipients were stratified into infection (n = 29) and non-infection (n = 16) groups. Pathogen detection rates, diagnostic performance metrics, donor-to-recipient transmission events, and mNGS-informed antimicrobial modifications were systematically analyzed.

RESULTS: Post-transplant infection occurred in 64.4% of recipients, predominantly involving the pulmonary compartment (89.7%). mNGS achieved significantly higher overall positivity rates than culture in both donors (95.6% vs. 80.0%) and recipients (64.4% vs. 22.2%), with superior detection of fungi and exclusive identification of all viral pathogens. The pathogen-level concordance between methods was predominantly partial (75%-78%). At the patient level, mNGS demonstrated a sensitivity of 69.0% versus 31.0% for culture, while culture maintained higher specificity (93.8% vs. 43.8%). A diverse pathogen landscape was identified, including Pneumocystis jirovecii, rare molds, cytomegalovirus (CMV), and Epstein-Barr virus (EBV)-all exclusively detected by mNGS. A total of 11 possible donor-to-recipient transmission events involving six pathogens were identified across 11 pairs, and 54.5% of affected recipients developed clinical infections, with Klebsiella pneumoniae accounting for the majority of transmission events. mNGS results informed antimicrobial treatment modifications in 69.0% of infected recipients. In the univariate analysis, liver cancer showed an exploratory association with lower post-transplant infection risk (OR = 0.10, 95%CI = 0.02-0.46, p = 0.003).

CONCLUSIONS: This retrospective matched-pair study suggests that mNGS substantially expands pathogen detection beyond conventional culture, enabling the identification of clinically relevant possible donor-derived pathogen transmission and informing antimicrobial treatment modifications in the majority of infected recipients. These findings support mNGS as an adjunctive peri-transplant diagnostic tool pending prospective multicenter validation.},
}

Humans
*Liver Transplantation/adverse effects
Retrospective Studies
*High-Throughput Nucleotide Sequencing
Female
*Metagenomics/methods
Male
Middle Aged
*Tissue Donors
*Transplant Recipients
*Anti-Infective Agents/therapeutic use
Adult

@article {pmid42974142,
year = {2026},
author = {He, Y and Huang, J and Du, B and Chen, Z and Huang, L and Shi, J and Zhang, M and Zhang, L and Tang, J},
title = {From sepsis to necrotizing enterocolitis with appendiceal perforation: a case report of successful salvage therapy with aztreonam-avibactam in an extremely preterm infant with NDM-producing Klebsiella pneumoniae.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1919037},
pmid = {42974142},
issn = {1663-9812},
abstract = {Infections caused by New Delhi metallo-β-lactamase (NDM)-producing Klebsiella pneumoniae represent a major therapeutic challenge in neonatology, particularly in extremely preterm infants, for whom effective options are limited and dosing and safety data for last-resort agents such as aztreonam-avibactam remain scarce. We report the case of a male infants born at 24[+2] weeks of gestation with a birth weight of 530 g who developed Klebsiella pneumoniae sepsis with poor clinical response to aztreonam combined with polymyxin B. His clinical course was complicated by pulmonary hemorrhage, disseminated intravascular coagulation, necrotizing enterocolitis, appendiceal perforation, and suspected necrotizing fasciitis. Blood and ascitic fluid metagenomic next-generation sequencing (mNGS) identified NDM-producing carbapenem-resistant K. pneumoniae. Given the lack of effective alternatives and ongoing clinical deterioration, off-label intravenous aztreonam-avibactam was initiated as salvage therapy. Marked clinical improvement was observed within 4 days after aztreonam-avibactam treatment, blood mNGS converted to negative by day 6, and skin and gastrointestinal manifestations resolved after 10 days of treatment, and no adverse events considered attributable to aztreonam-avibactam were identified. This case suggests that aztreonam-avibactam may be a viable salvage option for life-threatening NDM-producing K. pneumoniae infections in extremely preterm infants, though prospective pharmacokinetic and safety data in this population are urgently warranted.},
}

@article {pmid42974438,
year = {2026},
author = {Pruksangkul, S and Termsaithong, T and Mhuantong, W and Limpiyakorn, T and Sonthiphand, P},
title = {Effects of chemical fertilizer application on soil properties, banana (Musa paradisiaca) yields, and soil microbiomes in a long-term cultivation field.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21912},
pmid = {42974438},
issn = {2167-8359},
mesh = {*Musa/growth & development ; *Fertilizers/analysis ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil/chemistry ; Nitrogen/analysis ; Potassium/analysis ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Hydrogen-Ion Concentration ; Agriculture/methods ; },
abstract = {Due to climate change and increasing food demand, conventional agriculture relies heavily on chemical fertilizers. This study investigated the effects of chemical fertilizer application on soil properties, banana (Musa paradisiaca) yields, and soil microbiomes in a long-term cultivation field. Metagenomic analysis of the 16S rRNA gene provided a comprehensive overview of soil microbial diversity and functional potential. Nitrogen, phosphorus, and potassium (NPK) fertilizers at 0, 119, 238, and 476 kg ha[-1] were applied monthly for one year. Fertilizer application significantly altered soil properties and microbial community dynamics but had no significant effect on banana yields. Higher fertilizer rates reduced soil pH and increased available phosphorus and exchangeable potassium, while total nitrogen and organic matter remained relatively unchanged. Elevated NPK inputs increased the abundance of specific microbial taxa, including Bacillus, Streptomyces, uncultured bacterium JG30-KF-AS9, and Nitrospira, while Xanthobacteraceae, bacteriap25, Micromonosporaceae, Nocardioides, Subgroup 6, and Gemmatimonadaceae consistently represented core taxa across all treatments. Pearson's correlation analysis revealed that soil total nitrogen and exchangeable potassium were positively correlated with the abundance of key plant growth-promoting and nitrifying taxa, including Pseudomonas and Nitrospira, whereas soil pH was negatively correlated with Acidothermus, Nitrospira, and Bacillus, but positively correlated with Subgroup 6. Functional gene profiles further indicated enhanced anaerobic processes associated with carbon, nitrogen, and sulfur cycling. The findings suggest that long-term nutrient accumulation resulting from repeated fertilization and crop residue inputs may sustain banana crops throughout the 10-month production period without additional fertilization. Together, these findings highlight the need for fertilizer regimes tailored to long-term soil nutrient status, contributing to both sustainable agriculture and microbiome-informed crop management.},
}

*Musa/growth & development
*Fertilizers/analysis
*Soil Microbiology
*Microbiota/drug effects
*Soil/chemistry
Nitrogen/analysis
Potassium/analysis
Phosphorus/analysis
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Hydrogen-Ion Concentration
Agriculture/methods

@article {pmid42974475,
year = {2026},
author = {Ouyang, X and He, Y and Jin, Z and Wang, S and Zhao, G and Su, X and Du, J and Chen, Y and Tan, C and Li, X and Han, S and Wang, B and Zhao, J and Niu, J and Chen, C and Wang, J and Wang, C},
title = {Inhibition of ferroptosis by microbiota-derived lithocholic acid underlies the intestinal radioprotection of a host defensin-derived oligopeptide.},
journal = {iMeta},
volume = {5},
number = {1},
pages = {e70113},
pmid = {42974475},
issn = {2770-596X},
abstract = {Ionizing radiation-induced intestinal injury (IRIII) reduces survival in nuclear accident victims and compromises the efficacy of abdominal radiotherapy, and current treatment options remain limited. Human defensin 5 (HD5)-derived fragments are endogenous regulators of the gut microbiota, which affects host responses to radiation. However, whether these fragments influence intestinal radiosensitivity or can serve as lead compounds for IRIII therapeutics remains unclear. In this study, we investigated the role of HD5-derived fragments in IRIII and developed AT9(C/G), a potent radioprotective oligopeptide based on the lead fragment AT9. Fecal metagenomic and metabolomic analyses revealed that the oral administration of AT9(C/G) enriches Bifidobacterium pseudolongum and increases lithocholic acid (LCA) levels in the intestine. Both murine and clinical studies demonstrated a negative correlation between IRIII severity and fecal LCA levels. The radioprotective effect of LCA was further validated in both mouse models and human small intestinal organoids. Mechanistically, LCA suppresses ferroptosis in irradiated cells by remodeling lipid metabolism. Specifically, LCA activates Takeda G protein-coupled receptor 5 (TGR5), leading to the upregulation of sterol regulatory element-binding protein 1 (SREBP1), which transcriptionally modulates stearoyl-CoA desaturase 1 (SCD1) to catalyze monounsaturated fatty acid production. Pharmacological inhibition of SCD1 or genetic ablation of G-protein coupled bile acid receptor 1 (Gpbar1, encodes TGR5) attenuates the protective effects of AT9(C/G) in mice. This study establishes that an oligopeptide can modulate gut microbiota-derived LCA to confer intestinal radioprotection, presenting a promising preventive strategy against IRIII.},
}

@article {pmid42974490,
year = {2026},
author = {Zhang, Y and Lin, Z and Huang, R and Zhang, Y and Wang, L and Fu, Z and Wang, C and Xiao, S and Pramono, H and Xu, K and Xu, Z and Yin, Y},
title = {Nano-plastics disrupt systemic metabolism by remodeling the bile acid-microbiota axis and driving hepatic-intestinal dysfunction.},
journal = {iMeta},
volume = {5},
number = {1},
pages = {e70103},
pmid = {42974490},
issn = {2770-596X},
abstract = {The pervasiveness of microplastic pollution poses a growing health risk, yet its long-term metabolic consequences remain poorly defined. Here, we exposed mice to polyethylene terephthalate nanoparticle (NP) and combined histopathology, biochemistry, metabolomics, and metagenomics to resolve their interactions. NP ingestion induced a severe systemic phenotype characterized by weight loss, organ atrophy, dyslipidemia, and gut barrier collapse. Mechanistically, NPs disrupted bile acid (BA) homeostasis by hyperactivating hepatic synthesis pathways while suppressing microbial 7α-dehydroxylation. This accumulation of cytotoxic BAs drove hepatic lipogenesis and aggravated mucosal inflammation. Crucially, metagenomics uncovered significant gut microbiota dysbiosis, where the enrichment of bile salt hydrolase-encoding taxa and depletion of 7α-dehydroxylating clades reinforced this BA imbalance. Furthermore, the microbiota exhibited functional deterioration, shifting toward glycan degradation with a concurrent loss of antibiotic resistance genes, signaling reduced ecological resilience. These findings identify BA dysregulation and specific microbiota functional losses as primary drivers of NP-induced systemic metabolic collapse.},
}

@article {pmid42975132,
year = {2026},
author = {Salcedo, RSR and Jaffe, AL and Dekas, AE},
title = {Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0087826},
doi = {10.1128/msystems.00878-26},
pmid = {42975132},
issn = {2379-5077},
abstract = {Microbial chemoautotrophy has the potential to sustain ecosystems at depth, contribute to global carbon sequestration, and ameliorate the currently unbalanced marine carbon budget. However, an understanding of its mechanisms is still emerging, particularly beyond organisms performing nitrification. Here, we conduct a combined gene-based and genome-resolved analysis of 28 metagenomes from the Northeast Pacific Ocean to investigate the prevalence, distribution, and phylogenetic and metabolic diversity of marine chemoautotrophs. We find that organisms encoding marker genes for autotrophic dissolved inorganic carbon (DIC) fixation are abundant and widespread within our samples, comprising 11%-26% of microbial communities from 150 to 4,000 m water depth. Marker genes for the Calvin cycle and 3-hydroxypropionate bi-cycles are more prevalent than those for the 3-hydroxypropionate/4-hydroxybutyrate and reverse tricarboxylic acid cycles, the latter two of which are encoded by organisms conducting nitrification. We constructed and identified 128 putatively chemoautotrophic metagenome-assembled genomes (MAGs), spanning 13 phyla including the Proteobacteria, Actinobacteria, SAR324, and the Thermoproteota. These MAGs contain genes for the oxidation of carbon monoxide (77.3%), sulfur (69.5%), ammonia (5.5%), and/or methane (3.1%), suggesting that diverse catabolisms support deep-sea DIC fixation and an underappreciated potential role for aerobic carbon monoxide oxidation. Fifty percent of these MAGs encode multiple inorganic catabolic pathways, and 99% include genes for organic matter transport, suggesting catabolic flexibility and the use of externally produced organic matter, respectively. We create an inclusive inventory and map of potential chemoautotrophs at our study site, expanding their known phylogenetic breadth, metabolic repertoires, and potential to impact the carbon cycle.IMPORTANCEThe marine carbon cycle plays a central role in regulating ecosystem productivity and the global climate. Chemoautotrophy, the microbial conversion of inorganic carbon (e.g., CO2 or HCO3[-]) into cellular biomass, is an understudied process with the potential to significantly shift models of the marine carbon budget. While some marine chemoautotrophs are known, recent evidence suggests that the existing inventory is incomplete. Here, we find that microorganisms with the genetic potential for chemoautotrophy are more phylogenetically and metabolically diverse than previously appreciated. In particular, the prevalence of genes involved in CO oxidation suggests a potentially unrecognized role in supporting deep-sea chemoautotrophy. By identifying the potential microbial mediators and coupled energy sources, our results could aid future predictions of when, where, and how deep-sea chemoautotrophy occurs, and therefore its potential role in carbon cycling.},
}

@article {pmid42975317,
year = {2027},
author = {Gervais, A and Bastard, P and Bizien, L and Trespidi, F and Angelini, M and Rossini, G and Lazzarotto, T and Baldanti, F and Rovida, F and Ferrari, A and Mancon, A and Mileto, D and Cassaniti, I and Conti, F and Schmidt-Chanasit, J and Cadar, D and Florian, DM and Borghesi, A and Puel, A and Delifer, C and Tiberghien, P and de Lamballerie, X and Durand, GA and Aberle, JH and Nagy, A and Simonin, Y and Cobat, A and Zhang, SY and Casanova, JL},
title = {Type I IFN autoantibodies in three of seven Europeans with life-threatening Usutu virus infection.},
journal = {Journal of human immunity},
volume = {3},
number = {1},
pages = {},
pmid = {42975317},
issn = {3065-8993},
support = {/HHMI/Howard Hughes Medical Institute/United States ; //Rockefeller University/ ; //St. Giles Foundation/ ; //Stavros Niarchos Foundation/ ; R01AI163029/NH/NIH HHS/United States ; UL1TR001866/NH/NIH HHS/United States ; /TR/NCATS NIH HHS/United States ; ANR-10-IAHU-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; ANR-20-CE93-003//Agence Nationale de la Recherche/ ; ANR-22-CE15-0046//Agence Nationale de la Recherche/ ; ANR-21-RHUS-0008//Agence Nationale de la Recherche/ ; ANR-10-LABX-62-01//Agence Nationale de la Recherche/ ; GA 101191725//HORIZON-HLTH-2024-DISEASE-08-20/ ; EQU202503020018//French Foundation for Medical Research/ ; EA20170638020//French Foundation for Medical Research/ ; 101057100//HORIZON-HLTH-2021-DISEASE-04/ ; //Square Foundation/ ; //Grandir - Fonds de Solidarité Pour L'enfance/ ; //Fondation du Souffle/ ; //SCOR Corporate Foundation for Science/ ; //Institut National de la Santé et de la Recherche Médicale/ ; //Paris Cité University/ ; //Imagine Institute/ ; //Bettencourt-Schueller Foundation/ ; //ExposUM Institute/ ; //University of Montpellier/ ; ANRS0629//ANRS/ ; ANRS00869-R-PR//ANRS/ ; ANRS-23-PEPR-MIE-0007//ANRS/ ; //Battersea & Bowery Advisory Group/ ; //General Atlantic Foundation/ ; //REACTing-INSERM/ ; MESRI-COVID-19//French Ministry of Higher Education, Research, and Innovation/ ; },
abstract = {We previously reported that two of three patients with severe Usutu virus (USUV) disease carried circulating autoantibodies (auto-Abs) neutralizing type I IFNs (AAN-I-IFN). Here, we studied four additional patients, bringing the total number of European patients with life-threatening USUV infection to seven (Austria, n = 1; France, n = 1; Hungary, n = 4; Italy, n = 1). Three of these patients (all male, aged 43, 77, and 78 years, one French and two Hungarian) had blood auto-Abs neutralizing at least 10 ng/ml IFN-α2 and IFN-ω and at least 1 ng/ml IFN-β. They suffered from meningitis (n = 1), meningoencephalitis (n = 1), or myocarditis (n = 1). The other four patients were similar demographically and clinically but had no detectable AAN-I-IFN. No AAN-I-IFN were found in the 63 individuals with silent USUV infection tested (P = 6.4 × 10-4, Fisher's exact test). These AAN-I-IFN increased the risk of life-threatening USUV disease by 98.8-fold (95% CI: 4.12-2,369; P = 0.0046, Firth's bias-corrected logistic regression) and, thus, account for almost half the cases of life-threatening USUV infection in Europe.},
}

@article {pmid42975318,
year = {2026},
author = {Bajaj, JS and Davis, BC and Puri, P and Gallagher, ML and Fagan, A and Obolewicz, H and Mousel, T and Boja, SH and Sikaroodi, M and Gillevet, PM},
title = {Rifamycin use and gut microbial antibiotic resistance genes in cirrhosis: Results from a double-blind, placebo-controlled clinical trial.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2757339},
doi = {10.1080/19490976.2026.2757339},
pmid = {42975318},
issn = {1949-0984},
mesh = {Humans ; *Rifamycins/therapeutic use/pharmacology/administration & dosage ; Double-Blind Method ; *Liver Cirrhosis/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Female ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; Middle Aged ; Aged ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance gene (ARG) carriage is associated with poor outcomes in patients with liver cirrhosis, which is worsened by repeated antibiotic exposure and hospitalizations. While the semi-synthetic rifamycin derivative, rifaximin, has recently been linked to ARG expansion preclinically, the effects of rifamycin SV MMX (RiVM) on the gut resistome remain unknown. We evaluated longitudinal resistome changes with RiVM in cirrhosis. The randomized, double-blind, placebo-controlled RIVET trial (15 RiVM, 15 placebo) included compensated cirrhosis patients who underwent shotgun metagenomic sequencing before/after 30 days of therapy. ARGs were annotated using the Comprehensive Antibiotic Resistance Database. The longitudinal resistome was evaluated using univariable and multi-variable methods (LEfSe, paired-Wilcoxon testing, and MaAsLin3), and machine learning (ML) was used to determine ARG changes at subject and group levels. RiVM induced minimal perturbation of the gut resistome, without significant change in ARGs versus after FDR adjustment. Complementary approaches (univariable and multivariable) identified a trend towards lower vancomycin resistance ARGs, including vanW and vanT operon-associated genes, after RiVM exposure. In contrast, several Enterobacteriaceae-associated multidrug efflux regulators (including evgS, emrK, and mdtA) showed nominal increases post-rifamycin that did not withstand FDR. Group-level ML demonstrated limited discrimination between groups; however, within-subject longitudinal models achieved improved classification performance. No increase in infections or treatment-related safety concerns was observed. We conclude that rifamycin MMX was not associated with infections and did not enrich antimicrobial resistance genes compared to placebo in a small randomized 30-day clinical trial in patients with compensated cirrhosis. There was a tendency towards reduced vancomycin resistance and ARG reduction after rifamycin exposure. Registration: NCT04082780 www.clinicaltrials.gov.},
}

Humans
*Rifamycins/therapeutic use/pharmacology/administration & dosage
Double-Blind Method
*Liver Cirrhosis/microbiology/drug therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Female
*Bacteria/genetics/drug effects/isolation & purification/classification
*Gastrointestinal Microbiome/drug effects/genetics
Male
Middle Aged
Aged
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics

@article {pmid42975441,
year = {2026},
author = {Li, J and Liu, J and Cai, X and Mei, W and Jiang, L and Zhang, D and Li, B and Luo, C},
title = {Single-Cell Insights into Virus-Microbe Interactions in Emerging Contaminant Degradation.},
journal = {Environmental science & technology},
volume = {60},
number = {43},
pages = {30915-30926},
doi = {10.1021/acs.est.6c09032},
pmid = {42975441},
issn = {1520-5851},
support = {2026GXNSFAA00640245//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; 2023B1515020038//Natural Science Foundation of Guangdong Province/ ; 42277210//Natural Science Foundation of Guangdong Province/ ; 2023368//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 42477262//National Natural Science Foundation of China (NSFC)/ ; 42625707//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Biodegradation, Environmental ; Single-Cell Analysis ; },
abstract = {Viruses are increasingly recognized as critical regulators of microbial ecology, yet their roles in pollutant degradation remain largely unexplored. Here, we integrate Raman-activated cell sorting-stable isotope probing (RACS-SIP) and single-cell genomics to elucidate virus-microbe interactions underlying methylnaphthalene biodegradation in petroleum-contaminated soils. Microcosm experiments demonstrated up to 80% removal of methylnaphthalene within 36 days, accompanied by pronounced shifts in microbial and viral communities. Correlation analyses suggested potential virus-host associations, with Ochrobactrum and an unclassified Caudoviricetes phage emerging as key contributors to degradation. RACS-SIP enabled in situ identification and isolation of active degraders, and single-cell genomic analysis indicated that viral auxiliary metabolic genes, including methyltransferases, aldehyde dehydrogenases, and decarboxylases, may complement host pathways for the multistep conversion of methylnaphthalene to naphthalene. Subsequent mineralization occurs through canonical catechol and gentisate pathways encoded by the host genome. This study provides preliminary evidence that viruses may act as metabolic collaborators rather than passive parasites in pollutant degradation, potentially enhancing host metabolic capacity and influencing biodegradation outcomes. Beyond revealing a virus-inclusive metabolic network, the RACS-SIP framework overcomes key limitations of traditional metagenomic methods by resolving virus-host linkages at the single-cell level. These findings broaden our understanding of viral ecological functions and highlight novel leverage points for bioremediation technologies targeting emerging contaminants.},
}

Biodegradation, Environmental
Single-Cell Analysis

@article {pmid42975446,
year = {2026},
author = {Zhu, D and Gong, H and Zhou, S and Yang, J and Xie, L and Azari, M and Zheng, M and Dai, X},
title = {Public Goods Supply Structure Shapes Microbial Network Organization during Full-Scale Anammox Reactor Start-Up.},
journal = {Environmental science & technology},
volume = {60},
number = {43},
pages = {31020-31032},
doi = {10.1021/acs.est.6c06282},
pmid = {42975446},
issn = {1520-5851},
support = {24230712500//Shanghai Science International Cooperation Project/ ; 52470159//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Bioreactors/microbiology ; Oxidation-Reduction ; },
abstract = {Key public goods (KPGs) are metabolites or functions produced at a metabolic cost by microbial populations but potentially benefiting the community. In engineered anammox systems, such functions may underpin interdependencies between anaerobic ammonium-oxidizing bacteria (AnAOB) and associated microorganisms, yet their supply-side organization and temporal dynamics remain poorly understood. We integrated genome-resolved metagenomics and metatranscriptomics to quantify relative transcriptional contributions to 33 KPG biosynthesis pathways during start-up of a full-scale anammox reactor. Across 42 high-quality metagenome-assembled genomes (MAGs), these transcriptional contributions were used to infer supply structure and temporal evolution. Inferred KPG supply structures were highly uneven across stages (Gini = 0.74-0.98), with the top 20% of populations accounting for up to 98.7% of total transcriptional contribution. Three resource-specific trajectories emerged: progressively concentrated, persistently concentrated, and dynamically fluctuating supply. AnAOB dominated contributions associated with low-cost amino acids, acetate, nicotinamide adenine dinucleotide, coenzyme A, oxidative-stress defense, and extracellular polymeric substance export potential, but showed apparent dependence on non-AnAOB populations for vitamins, cofactors, and high-cost amino acids. Restructuring was driven mainly by redistribution among retained populations rather than supplier turnover, with the strongest reorganization occurring during early start-up. These findings reveal a structured, resource-dependent, and dynamically reorganized KPG landscape during reactor establishment.},
}

*Bioreactors/microbiology
Oxidation-Reduction

@article {pmid42975948,
year = {2026},
author = {Ring, N and Low, AS and Evans, R and Keith, M and Paterson, GK and Gally, D and Nuttall, T and Clements, DN and Fitzgerald, JR},
title = {Benchmarking nanopore-based strategies for antimicrobial resistance prediction.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
pmid = {42975948},
issn = {2057-5858},
mesh = {*Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests/methods ; *Nanopores ; Humans ; Benchmarking ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Computer Simulation ; Whole Genome Sequencing/methods ; Genome, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) presents a pressing need to ensure that the right antimicrobials are used to target the right microbes at the right time. Ideally, the appropriate antimicrobial is selected after patient samples have been cultured and assessed with antimicrobial sensitivity testing (AST). However, the time needed for culture-based diagnosis leads to immediate empirical treatment, often with broad-spectrum and/or high-tier antimicrobials. Direct nanopore metagenomic whole-genome sequencing to identify pathogens and predict their AMR is a rapid and patient-side alternative. A limitation of this approach is potential inconsistencies in i predicted AMR phenotypes. Here, we benchmarked the current performance of in silico AMR prediction strategies for nanopore-generated long-read data. Using real-world nanopore data paired with AST phenotyping for 201 samples representing 27 bacterial species, we assessed the impact of basecalling mode, data volume and assembly strategy and compared the performance of eight in silico AMR prediction tools with seven AMR databases. We found that basecalling accuracy mode does not significantly affect the overall accuracy of in silico AMR predictions but assembly strategy and data volume both do. Prediction tools using the ResFinder database scored best for balanced accuracy (0.80±0.02 for both ResFinder and ABRicate), whilst DeepARG scored best for sensitivity (0.65±0.03); predictions were more accurate for some antibiotic classes and genera than others. However, even the best-performing in silico AMR prediction strategy missed some resistance identified by lab-based AST. We conclude, therefore, that currently in silico AMR prediction can supplement lab-based AST but cannot yet replace it.},
}

*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests/methods
*Nanopores
Humans
Benchmarking
*Nanopore Sequencing/methods
Metagenomics/methods
Computer Simulation
Whole Genome Sequencing/methods
Genome, Bacterial

@article {pmid42976166,
year = {2026},
author = {López-Gutiérrez, S and Espinosa-Barrera, LA and Soto-Hernández, A and Zuleta-Prada, H and Bustos-Brito, C and Cardona-Félix, CS and Utrilla, J and Velazquez-Cruz, B and Cárdenas-Conejo, Y and Araujo-León, JA and Aguilar-Hernández, V and Osuna-Castro, JA and Esquivel, B and Serrano-Posada, H and Centeno-Leija, S},
title = {A Baltic Sea microbiome-derived Type III polyketide synthase produces host-protective alkylresorcinols in E. coli.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0361965},
doi = {10.1371/journal.pone.0361965},
pmid = {42976166},
issn = {1932-6203},
mesh = {*Escherichia coli/metabolism/genetics ; *Polyketide Synthases/metabolism/genetics/chemistry ; *Resorcinols/metabolism/chemistry ; *Microbiota ; },
abstract = {Marine microorganisms are a prolific source of novel polyketide synthases (PKSs) that generate structurally diverse and functional polyketides. Here, we identify a novel type III PKS, ArsMB, from Pontimonas sp. via metagenomic mining of a Baltic Sea microbiome. Heterologous expression of arsMB synthetic gene in an Escherichia coli host that lacks a native type III PKS, combined with a two-step strategy to boost acyl-CoA precursor availability in a glucose-mineral medium, enabled the in vivo synthesis of two cell-associated alkylresorcinols, identified by GC-MS as 5-pentadecyl-1,3-benzenediol (ars1) and 5-tridecyl-1,3-benzenediol (ars2). The product profile is consistent with a tetraketide alkylresorcinol biosynthetic pathway utilizing C16 and C14 acyl starter units, drawn from the host acyl-CoA pool. In agreement, AlphaFold2-based structural modeling predicts a Cys139/His275/Asn308 catalytic triad and a long hydrophobic substrate tunnel compatible with long-chain acyl starter units. E. coli producing the amphipathic cell-associated alkylresorcinols ars1/ars2 exhibited increased resistance to muralytic digestion by endolysins and to hydrogen peroxide. These findings expand the known repertoire of marine-derived type III PKSs and highlight the biotechnological potential of ArsMB-derived alkylresorcinols.},
}

*Escherichia coli/metabolism/genetics
*Polyketide Synthases/metabolism/genetics/chemistry
*Resorcinols/metabolism/chemistry
*Microbiota

@article {pmid42976318,
year = {2026},
author = {Gray, K and Benis, A and Dueholm Müller, S and Winkel, K and Borda, A},
title = {Informatics for the Planet: Integrating Species, Ecosystems, and Geophysical Data to Manage the Health of Earth Systems.},
journal = {JMIR medical informatics},
volume = {14},
number = {},
pages = {e113778},
doi = {10.2196/113778},
pmid = {42976318},
issn = {2291-9694},
mesh = {*Ecosystem ; *Earth, Planet ; Humans ; *Medical Informatics ; Climate Change ; },
abstract = {Biomedical and health informatics has traditionally focused on human-centric clinical data to support individual patient care and health systems. However, contemporary health challenges driven by climate change, biodiversity loss, and ecological degradation demand an expanded paradigm that addresses interdependencies among human, animal, and environmental health. This editorial introduces a new JMIR Medical Informatics section called "Planetary Health Informatics"-an essential evolution extending informatics praxis beyond human health care and toward Earth's interconnected systems. JMIR Medical Informatics is launching a call for papers for this new section dedicated to advancing planetary health informatics (PHI) theory, methods, and applications for a sustainable future shaped by humans' impact on Earth. We invite authors to submit work that explores how PHI integrates species, ecosystem, and geophysical data to address critical global challenges, including metagenomic disease surveillance, climate-related hazard forecasting, environmental pollution monitoring, and health infrastructure decarbonization. By synthesizing broader ecological frameworks, we present a road map for transforming fragmented data streams into planetary-scale intelligence.},
}

*Ecosystem
*Earth, Planet
Humans
*Medical Informatics
Climate Change

@article {pmid42976505,
year = {2026},
author = {Kalt, M and Poltorak, V and Mastrorilli, E and Ceppi, E and Yu, Y and Zimmermann, M and Sunagawa, S and Robinson, SL and Fenner, K},
title = {Assessing field-scale effects of treated wastewater on riverine biofilms: Community composition, functional genes, and micropollutant biotransformation.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127197},
doi = {10.1016/j.watres.2026.127197},
pmid = {42976505},
issn = {1879-2448},
abstract = {Treated wastewater (WW) released from wastewater treatment plants (WWTPs) leads to the influx of microorganisms and micropollutants (MPs) into receiving waters, and hence presents a continuous anthropogenic pressure on downstream riverine microbial communities; however, its impact on their composition and function remains insufficiently understood, particularly under environmentally realistic field conditions spanning multiple rivers, seasons, and wastewater treatment technologies. In this study, we investigated the effects of treated WW effluent on microbial community composition, functional profiles, the prevalence of antibiotic resistance genes (ARGs), and the fate of 189 MPs in riverine biofilms, including detailed biotransformation analyses for 122 reliably quantifiable MPs. Biofilms were grown under well-characterized field conditions across six Swiss rivers receiving effluent from WWTPs that varied in treatment technology, wastewater dilution, and season. At each river, pairs of biofilms were grown and collected at two sites upstream (up) and three sites downstream (dw) of the WWTP discharge point, resulting in a total of 60 biofilm communities. At the level of overall community composition and general functional profiles, differences between up- and downstream sites were inconsistent. However, clearer differences emerged when analyses focused on non-dominant taxa and specific functional traits, such as ARGs and MP biotransformation, indicating subtle but ecologically relevant impacts of treated WW that may be masked by broader trends. Approximately half of the analyzable MPs were measurably biotransformed, with the majority of these transformations likely occurring via co-metabolic processes, as suggested by MP structures and overall low variance in biotransformation rate constants. For a few MPs, which had previously been associated with catabolic biodegradation, enhanced biotransformation potential was detected in 8 out of 36 downstream biofilms. These observations of increased downstream biotransformation were predominantly associated with moving bed biofilm reactor (MBBR)-based WWTPs, suggesting that WW effects were highly technology-specific rather than ubiquitous. Fine-grained metagenomic analysis revealed an association between the abundance of relevant Enzyme Commission (EC) classes and enhanced saccharin biotransformation in downstream biofilms. While increased downstream biotransformation was heterogeneous and infrequent, multiple lines of evidence suggest that microbes transferred from the WWTP via treated WW effluent endowed these functions to downstream biofilms. Overall, our findings show that WWTP impacts on riverine biofilms are generally subtle at the level of overall community structure but become apparent when focusing on non-dominant taxa and specialized functional traits, which play a disproportionate role in shaping MP biotransformation potential.},
}

@article {pmid42976520,
year = {2026},
author = {Yue, Y and Yuan, M and Fan, Z and Shan, L and Zhao, Y and He, C and Ma, Q and Zhang, L},
title = {A synthetic microbial community derived from the roots of Kalidium gracile enhances its salt tolerance by modulating gene transcription and reshaping the rhizosphere soil microbiota.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128805},
doi = {10.1016/j.micres.2026.128805},
pmid = {42976520},
issn = {1618-0623},
abstract = {Soil salinization and alkalinization are severe environmental problems in the desert-oasis transition zone of the Hexi Corridor, China. Rhizosphere microbial communities are key regulators of plant adaptation to saline-alkali environments. However, the functional microbial resources and ecological mechanisms underlying the contribution of the rhizosphere microbiome associated with Kalidium gracile to its saline adaptation remain poorly understood. In this study, we characterized the rhizosphere microbiome of K. gracile inhabiting severely saline-alkali soil and isolated two Bacillus strains with strong plant growth-promoting potential, which were subsequently used to construct a synthetic microbial community (SynCom). Inoculation experiments under salt stress demonstrated that SynCom increased plant biomass and chlorophyll content and modulated host transcriptional responses associated with the "growth-defense trade-off." Shortly after inoculation, plant growth-related pathways were suppressed, while CAT and POD activities surged by 45% and 213%, respectively. At later stages after inoculation, the expression of growth-related pathways was significantly upregulated. Metagenomic sequencing revealed that SynCom reshaped the rhizosphere microbial community, with the relative abundances of the halophilic bacteria Halomonas and Marinobacter increasing by 317% and 1162%, respectively. The abundances of functional genes involved in soil carbon, nitrogen, phosphorus, and sulfur nutrient cycling were all significantly increased. Collectively, these findings indicate that SynCom enhances plant salt tolerance through a multi-layered regulatory mechanism by coordinating host physiological responses and rhizosphere microbial functions. Collectively, these findings reveal a multi-level regulatory mechanism through which SynCom enhances plant salt tolerance by coordinating host physiological responses and rhizosphere microbiome functions.},
}

@article {pmid42976543,
year = {2026},
author = {Lu, HB},
title = {Description of 10 novel species within genus Janthinobacterium isolated from alpine lakes.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126784},
doi = {10.1016/j.syapm.2026.126784},
pmid = {42976543},
issn = {1618-0984},
abstract = {Strains of genus Janthinobacterium are cosmopolitan and widely found in glaciers. As glaciers retreated, numerous lakes developed in alpine regions. It remains unknown whether Janthinobacterium strains inhabit these lakes. Numerous small freshwater lakes, formed following Quaternary glaciation, occur in the mountainous regions of Southwest China. Metagenomic approaches combined with isolation and cultivation methods are applied to investigate Janthinobacterium strains from seven alpine lakes in this region. The annotated reads using Kraken 2 reveal that the mean relative abundance of genus Janthinobacterium is 0.27%, but no metagenome-assembled genomes are recovered for this genus. Though 11 Janthinobacterium strains are isolated from these alpine lakes, none of the metagenomic reads could be mapped to these isolates. Nevertheless, the ANI, AAI, digital DDH and phylogenomic analyses support that these 11 isolated strains should represent 10 novel species of genus Janthinobacterium, for which the names Janthinobacterium altilacustre sp. nov., Janthinobacterium alpinum sp. nov., Janthinobacterium cryophilum sp. nov., Janthinobacterium lacus sp. nov., Janthinobacterium limneticum sp. nov., Janthinobacterium limnophilum sp. nov., Janthinobacterium montanilacus sp. nov., Janthinobacterium montanum sp. nov., Janthinobacterium oligotrophicum sp. nov. and Janthinobacterium yunnanense sp. nov. are proposed. Comparative genomic analyses further reveal that Janthinobacterium strains possess strong phosphorus metabolic potential but exhibit distinct capacities for nitrogen metabolism. Strains isolated from alpine lakes also harbor unique genetic traits, such as hydrogen metabolism. Taken together, this study expands our understanding of the ecological function potential of Janthinobacterium strains.},
}

@article {pmid42963094,
year = {2026},
author = {Hong, C and Nguyen, TP and Ngo, HHH and Le, HT and Vu, TT and van Wijk, M and Umenthala, SR and Batheja, D and Otuko, R and Naing, SY and Wagenaar, J and Cooper, B and Kesteman, T and van Doorn, R and Moon, K and Bui, DD and Imbach, P and Lewycka, S},
title = {Directional spillover of antimicrobial-resistant bacteria from animal, food-production and environmental reservoirs to humans: protocol for a systematic scoping review and causal evidence assessment.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e125301},
pmid = {42963094},
issn = {2044-6055},
abstract = {INTRODUCTION: Transmission of antimicrobial-resistant bacteria from animal, food-production and environmental reservoirs to humans underpins One Health policy, yet the causal evidence has not been systematically assessed. Molecular similarity is often invoked as evidence of transmission, but shared resistance determinants cannot establish the direction of transfer. This review will identify and classify evidence on antimicrobial resistance transmission from these reservoirs to humans, generate an evidence map by reservoir category and transmission pathway and identify gaps where policy assumptions outpace empirical support.

METHODS AND ANALYSIS: This systematic scoping review will be reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). We searched MEDLINE, Embase, Web of Science, Scopus, Global Health and China National Knowledge Infrastructure from 2000 onwards (initial search 16 July 2026; supplementary search 20 September 2026), supplemented by grey literature and citation tracking. Studies linking these reservoirs to human colonisation or infection with antimicrobial-resistant bacteria will be eligible. Records will be screened in duplicate in Rayyan with AI-assisted prioritisation (MetaScreener). Two reviewers will independently assess causal support using a framework integrating evidence type, directionality and level assignment, informed by Grading of Recommendations Assessment, Development and Evalution (GRADE) principles and Bradford Hill criteria. Strain-level and gene-level evidence (including metagenomic signals) will be distinguished, and colonisation and infection will be coded as parallel outcomes. The primary output will be a 9×5 evidence map crossing reservoir categories with transmission pathways, showing the highest causal support level, study counts and directionality for each combination.

ETHICS AND DISSEMINATION: This review analyses existing published data; ethical approval is not required. Findings will be submitted to a peer-reviewed open-access journal, presented at conferences and summarised as briefing materials for One Health policy bodies. The evidence map, extraction dataset and analytic code will be made publicly available through the Open Science Framework (OSF).

REGISTRATION: This protocol is registered on the OSF; registration Digital Object Identifier (DOI): 10.17605/OSF.IO/KQVDC.},
}

@article {pmid42966262,
year = {2026},
author = {Mi, X and Wang, Z and Ran, M and Shi, B and Wang, H},
title = {Coupled physicochemical and microbial recovery of aged premise plumbing following water-supply interruption.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127227},
doi = {10.1016/j.watres.2026.127227},
pmid = {42966262},
issn = {1879-2448},
abstract = {Water-supply interruptions can cause pronounced deterioration of premise-plumbing water quality, yet the coordinated responses of bacterial communities, antibiotic resistance, bacteriophages, and microbial functional potential during water-supply resumption remain poorly resolved. Here, a full-scale 24-h water-supply interruption in an approximately 25-year-old cast-iron premise-plumbing system was investigated by integrating physicochemical measurements, quantitative PCR, metagenomics, virus-host prediction, and functional analyses. At 1 min after water supply resumption, residual chlorine was undetectable, whereas turbidity and total iron ranged from 149.9 to 155.3 NTU and 13.4 to 13.8 mg/L, respectively. By 40 min, residual chlorine reached 0.52 to 0.56 mg/L, while turbidity and total iron declined to levels of 0.56 to 0.61 NTU and 0.028 to 0.041 mg/L, respectively. Concurrently, Legionella pneumophila decreased from 4.12 to 0.83 log10 (gene copies/mL), and mexA from 5.55 to 1.77 log10 (gene copies/mL). Metagenomic analyses revealed pronounced succession of bacterial communities, putative human pathogen-associated taxa, and the resistome. Caudoviricetes dominated the viral community and showed coordinated temporal changes with predicted bacterial hosts. Biofilm-associated functional genes, extracellular polymeric substances (EPS), and putative phage-encoded auxiliary metabolic genes were more abundant in the initially discharged water and generally decreased following water supply resumption. The elevated EPS may have reflected both microbial production and detachment of pre-existing biofilm-associated material. Collectively, the results identify the initially discharged water as a distinct post-stagnation physicochemical and microbiological state. Water-supply resumption represents a rapid ecological transition in which restoration of disinfectant residual and displacement of stagnant/pipe-associated material jointly restructure the microbiome, resistome, and virome.},
}

@article {pmid42966315,
year = {2026},
author = {Martins, GL and de Freitas, AS and Pellegrinetti, TA and Alexandre, LF and Lange, DF and Finck, J and Hanada, RE and Mendes, LW and Gleixner, G and Tsai, SM},
title = {Agroforestry development drives a progressive shift from physicochemical to microbially mediated organic matter cycling in tropical soils.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131266},
doi = {10.1016/j.jenvman.2026.131266},
pmid = {42966315},
issn = {1095-8630},
abstract = {Land-use change in tropical soils alters dissolved organic matter (DOM) chemistry and carbon cycling, however, linkages to microbial functions remain unresolved. We tested whether microbial carbon-degradation potential is associated with DOM composition along an Amazonian agroforestry chronosequence (10, 20, and 30 years), using adjacent pasture and primary forest as references. We integrated shotgun metagenomics with high-resolution mass spectrometry to couple carbohydrate-active enzyme (CAZymes) profiles to DOM composition. Soil chemistry explained 41.6% of the variability in microbial composition, while land-use type accounted for 28.5% of DOM variability. Seasonality did not affect microbial composition but was a significant source of variation in DOM. Relative to pasture, agroforests showed higher potential for sucrose and α-glucan degradation and a greater abundance of aliphatic DOM, indicating enhanced microbial processing. Older agroforests were enriched in genes targeting lignin and microbial-derived substrates such as peptidoglycan, resembling primary forest, whereas younger agroforests had higher abundances of GH36, GH5, and CE3 genes linked to cellulose and hemicellulose degradation, resembling pasture. Soil pH and available P were marginally associated with microbial-derived compound degradation, while pH, P, and Ca showed a stronger association with plant-derived compound processing. These results suggest that as agroforestry develops, carbon cycling may shift from physicochemical to microbial regulation, while DOM remained related to vegetation inputs and seasonality. Soil management of pH and available P during early establishment could support this transition, but the recovery may take decades.},
}

@article {pmid42966464,
year = {2026},
author = {Liu, ZW and Lai, CH and Gan, RY and Chen, L and Zhang, BB and Cheng, WY and Dong, XL and Wong, KH},
title = {The stimulative effect of Cordyceps sinensis functionalized selenium nanoparticles on bone development in growing mice: involvement of the gut microbiota-bone axis.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.10.054},
pmid = {42966464},
issn = {2090-1224},
abstract = {INTRODUCTION: Achieving optimal peak bone mass (PBM) during adolescence through adequate intake of trace element such as selenium is crucial for reducing osteoporosis risk in later life. We previously developed novel functionalized selenium nanoparticles (Cs4-SeNPs) utilizing polysaccharide-protein complex isolated from Cordyceps sinensis for prevention of osteoporosis. The gut microbiota, functioning as the "second gene pool", plays a crucial role in maintaining bone homeostasis. However, how Cs4-SeNPs regulate bone metabolism via the gut microbiota-bone axis remains unclear.

OBJECTIVES: To elucidate how the gut microbiota and microbial metabolites mediate the bone-promoting effect of Cs4-SeNPs.

METHODS: Growing mice model was used to assess the effect of Cs4-SeNPs on bone development. Metagenomics, metabolomics, and proteomics analyses were conducted to uncover the mechanism of action of Cs4-SeNPs. In vitro osteoblast and osteoclast models were employed to validate the effects of key gut microbial metabolites regulated by Cs4-SeNPs on osteogenesis and osteoclastogenesis. Pseudo-germ-free mice model treated with antibiotics was employed to determine the role of gut microbiota in bone-promoting effects of Cs4-SeNPs.

RESULTS: We found that Cs4-SeNPs significantly enhanced bone mass in growing mice, as evidenced by improved bone microarchitecture and increased expression of bone extracellular matrix-related markers. Notably, antibiotic treatment-induced microbial depletion abolished the effects of Cs4-SeNPs on bone development in growing mice. Increased abundance of beneficial gut bacterial genera, notably Adlercreutzia and Parvibacter, were observed following Cs4-SeNPs administration. Proteomics analysis and subsequent verification experiments demonstrated that Cs4-SeNPs inhibited the TNF-R1/TAB2/NF-κB inflammatory pathway and upregulated the expression of antioxidant proteins including SERPINA3K, GPX1, and SOD in the bone tissue. Metabolomic analysis revealed that Cs4-SeNPs treatment significantly elevated fecal and serum levels of two key metabolites: kynurenic acid and trehalose. Further in vitro studies confirmed that kynurenic acid and trehalose could reproduce the effects of Cs4-SeNPs on osteoblastic and osteoclastic differentiation.

CONCLUSIONS: Our findings suggest that Cs4-SeNPs optimize PBM and promote bone development in growing mice by improving the osteoblast/osteoclast balance via the modulation of the inflammatory TNF-R1/TAB2/NF-κB axis and the enhancement of antioxidant activity through the elevated levels of gut microbial metabolites kynurenic acid and trehalose in a gut microbiota-dependent manner.},
}

@article {pmid42966544,
year = {2026},
author = {Tang, J and Sun, B and Wang, Y and Chen, H and Zheng, W and Lin, H and Luo, Y and Zeng, Z and Chu, N and Zeng, RJ and Shen, R and Jiang, Y},
title = {Bridging CO2 electroreduction and microbial chain elongation toward C4-C6 carboxylic acids using formate and ethanol.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136176},
doi = {10.1016/j.biortech.2026.136176},
pmid = {42966544},
issn = {1873-2976},
abstract = {High-value conversion of CO2 through staged electrochemical-biological processes remains challenging because direct electrochemical synthesis of long-chain products involves complex reaction pathways and competing reactions. Microbial chain elongation provides an alternative route for upgrading low-carbon intermediates, but suitable bridging substrates are needed to connect upstream CO2 conversion with downstream microbial metabolism. Here, we developed a staged electrochemical-biological platform using formate and ethanol as bridging substrates. A Cu-Ag gas-diffusion electrode integrated with a solid-state electrolyte reactor enabled electrolyte-free co-production of formate and ethanol from CO2. At 300 mA cm[-2], the Faradaic efficiencies of formate and ethanol remained above 23 % and 17 %, respectively, over 30 h. A synthetic electrolyte-free formate-ethanol mixture was then used as a defined co-substrate for microbial upgrading. Compared with acetate-ethanol, formate-ethanol was associated with greater butyrate accumulation but lower caproate formation. Microbial community and metagenomic analyses revealed distinct community compositions and genetic potentials related to co-substrate conversion and chain-elongation functions. This study provides evidence that formate-derived carbon is incorporated during microbial chain elongation, linking CO2 electroreduction with C4-C6 carboxylic acid production and offering a potential framework for coupling electrochemical carbon conversion with microbial product upgrading.},
}

@article {pmid42966545,
year = {2026},
author = {Wu, S and Quan, Y and Gao, F and Shi, L and Liu, Z and Shen, Z and Elsayed Ali, EA and Veeramuthu, A and Chen, H},
title = {Metagenomic insights into microbial adaptation and resilience of single-stage partial nitritation-anammox systems assisted by graphene oxide sponges under increasing salinity.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136174},
doi = {10.1016/j.biortech.2026.136174},
pmid = {42966545},
issn = {1873-2976},
abstract = {Salinity is an increasingly important challenge limiting the application of single-stage partial nitritation-Anammox (PN/A) processes for treating saline nitrogen-rich wastewaters due to osmotic stress and microbial activity inhibition. In this study, a graphene oxide sponge (GOS)-assisted PN/A system was operated for 164 days under progressively increasing salinity from 2,000 to 12,000 mg/L NaCl to investigate the long-term performance and the associated physiological, ecological, and functional responses to salinity stress. Despite transient performance deterioration following each salinity increment, the reactor rapidly acclimated and maintained stable nitrogen removal, achieving ammonia removal efficiencies above 98%. Salinity acclimation promoted extracellular polymeric substance (EPS) production, particularly tightly bound EPS, and enhanced the activities of ammonia-oxidizing bacteria and anammox bacteria. Scanning electron microscopy confirmed dense biofilm formation on the GOS, while elemental analysis indicated a lower surface-associated sodium signal in the attached biomass compared with suspended sludge. Microbial community analysis revealed the enrichment of salt-tolerant functional microorganisms, particularly Candidatus Kuenenia and Nitrosomonas. Metagenomic analysis further demonstrated that microbial adaptation was primarily associated with the enrichment of genes involved in two-component systems, ABC transporters, and quorum sensing pathways, suggesting increased functional potential for environmental sensing, transport regulation, and microbial communication, while the nitrogen transformation pathways remained relatively stable. These findings characterize the long-term performance and associated microbial responses of a GOS-assisted PN/A system under progressive salinity stress, providing new mechanistic insights into the salinity resilience of PN/A systems treating saline nitrogen-rich wastewaters.},
}

@article {pmid42966564,
year = {2026},
author = {Li, Z and Shi, B and Luo, N and Zhao, C and Weng, Q and Chen, J and Wang, M and Zhu, D},
title = {Metagenomic Features of Oral Microbiome in Tibetan Dental Caries Patients: An Exploratory Study.},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {},
number = {},
pages = {103062},
doi = {10.1016/j.jormas.2026.103062},
pmid = {42966564},
issn = {2468-7855},
abstract = {OBJECTIVE: This study aimed to preliminarily explore the composition and functional potential of oral bacteria in Tibetan patients with dental caries, and to explore potential associations between the observed functional features and the high-altitude living environment and dietary habits.

METHODS: Saliva samples were collected from nine Tibetan individuals with dental caries. Sequencing was performed on an Illumina high-throughput sequencing platform. The obtained genomes were annotated and analyzed using the non-redundant protein (nr) database, Clusters of Orthologous Genes (COG) database, Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active Enzymes (CAZy) database, Comprehensive Antibiotic Resistance Database (CARD), and Virulence Factor Database (VFDB).

RESULTS: Across the nine samples, seven dominant phyla and ten dominant genera were identified. At the phylum level, Bacillota (44.06%) and Actinomycetota (26.2%) were predominant. At the genus level, Streptococcus (25.96%) predominated. Functional annotation showed that genes and pathways linked to cell wall/membrane biogenesis (32,623 genes) and carbohydrate metabolism (39,616 genes) accounted for a notable proportion of the total, thereby forming an efficient metabolic cascade encompassing carbohydrate uptake, metabolism, and acid production. Furthermore, multidrug resistance-related annotations represented the largest CARD category (53.05%), whereas immune modulation-related annotations predominated in VFDB annotation (52.48%).

CONCLUSIONS: This study provides a preliminary description of the community composition and functional annotation features of the oral microbiome in Tibetan patients with dental caries, showing prominent annotations related to carbohydrate metabolism and biofilm-associated functions, as well as resistance- and virulence-related annotations. These exploratory findings may serve as an initial reference for future studies on dental caries in Tibetan communities using larger cohorts and experimental validation.},
}

@article {pmid42966623,
year = {2026},
author = {Justine, M and Bargheet, A and Blomberg, B and Moyo, SJ and Gidabayda, JG and Löhr, IH and Lukumay, S and Pettersen, VK and Langeland, N and Klingenberg, C},
title = {Probiotics and diarrhoea morbidity among infants in Tanzania: secondary analysis of a randomised clinical trial.},
journal = {BMJ paediatrics open},
volume = {10},
number = {1},
pages = {},
pmid = {42966623},
issn = {2399-9772},
abstract = {INTRODUCTION: Diarrhoea causes annually more than 444 000 deaths in children globally, the majority in infants in low-income countries. The gut microbiota is a key determinant in resilience against enteric infections. We evaluated the effects of Bifidobacterium-based probiotic supplementation on diarrhoea morbidity among infants in Tanzania and explored associations between the gut microbiota composition at 6 weeks of age and later diarrhoeal risk.

METHODS: Secondary analysis of a double-blind, placebo-controlled randomised trial including infants in rural Tanzania between 1 February 2022 and 4 January 2023. 2000 participants were enrolled and randomly assigned to probiotics (n=1000) or placebo (n=1000), starting within the first 3 days of life and administered daily by caregivers in the first 4 weeks of life. Stool samples for gut microbiota analyses were collected 6 weeks after birth. The primary outcome was rate and duration of diarrhoea until 6 months of age. Secondary outcomes were associations between gut microbiota composition at 6 weeks of age and subsequent risk of diarrhoea.

RESULTS: Among 1945 infants with 6-month follow-up data, 126 infants developed diarrhoea, with no significant difference in rates between probiotic (53/970, 5.5%) or placebo (73/975, 7.5%) groups, p=0.070. Total days with diarrhoea were lower in the probiotic group (638 days) than in the placebo group (1057 days), p=0.048. Persistent diarrhoea (>14 days) occurred less frequently in the probiotic group (13%) versus placebo group (29%), p=0.038. A metagenomic comparison of 100 diarrhoea cases and 235 non-diarrhoea matched controls revealed significantly different taxonomic profiles between infants who later developed diarrhoea and those who did not. Enteric pathobionts were enriched, and lactic acid-producing commensals depleted among diarrhoea cases.

CONCLUSION: Early-life probiotic supplementation was associated with lower total days of diarrhoea and a lower occurrence of persistent diarrhoea, but not with significantly lower rates of diarrhoea between probiotic and placebo groups. Differences in early gut microbiota preceding illness suggest that the microbial composition may impact susceptibility to diarrhoeal disease.

TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT04172012.},
}