@article {pmid42879867,
year = {2026},
author = {Gao, Y and Xu, J and Bi, X and Xiang, W and Chen, D and Huo, H},
title = {Iron-functionalized carbonized melamine sponge reinforces aerobic granular sludge and reconfigures nitrogen-metabolic potential.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127128},
doi = {10.1016/j.watres.2026.127128},
pmid = {42879867},
issn = {1879-2448},
abstract = {Aerobic granular sludge (AGS) is limited by slow granulation and structural instability under variable municipal wastewater conditions. Here, an iron-functionalized carbonized melamine sponge (Fe[3+]@CMS) was developed as a three-dimensional scaffold to accelerate granulation and improve nitrogen removal. Fe[3+]@CMS reduced the time required for complete granulation by 20 d and became embedded within the granules as a persistent internal skeleton. It promoted extracellular polymeric substance (EPS) production during granule nucleation, whereas mature Fe[3+]@CMS-supported granules maintained greater structural integrity with lower EPS accumulation, suggesting partial substitution for the native EPS-dependent framework. After transition to real municipal wastewater, the Fe[3+]@CMS reactor maintained an average soluble COD removal of 92.4% and >97% ammonium removal, and achieved a final total nitrogen removal efficiency of 84.45%, compared with 44.10% in the control. Fe[3+]@CMS also suppressed excessive Thiothrix proliferation and favored denitrifying and iron-redox-associated taxa. Metagenomic analysis indicated selective redistribution rather than overall enrichment of nitrogen-cycle genes: napA/napB and nirS showed higher relative abundances, while the DNRA/(nirK + nirS) abundance ratio decreased from 0.184 to 0.107. These findings demonstrate that Fe[3+]@CMS acts as both a persistent structural scaffold and a selective ecological niche, integrating aerobic-granule stabilization with enhanced denitrification under fluctuating wastewater conditions.},
}

@article {pmid42880064,
year = {2026},
author = {Sun, P and Tan, Y and Jia, R and Lian, J and Yang, T and Li, H and Zhu, Z and Xi, C},
title = {Impacts and mechanisms of oyster farming on denitrification and anammox in coastal sediments from Tieshan Bay, China.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108453},
doi = {10.1016/j.marenvres.2026.108453},
pmid = {42880064},
issn = {1879-0291},
abstract = {Oyster aquaculture is widely recognized as an effective way to mitigate coastal eutrophication, but critical knowledge gaps remain regarding how it modulates nitrogen removal processes, which requires further investigation. In this study, sediments from oyster farming (OY) and non-oyster farming (NOY) areas in Tieshan Bay, China, were analyzed to explore the impacts of oyster farming on denitrification and anammox in coastal sediments. OY sediments exhibited significantly higher sediment oxygen demand (SOD), total organic carbon (TOC), ammonium (NH4[+]), ferrous iron (Fe[2+]), and sulfide than NOY sediments (P < 0.05), collectively creating hypoxic conditions favorable for nitrogen removal. Denitrification dominated nitrogen removal in both areas (OY: 91.84%; NOY: 90.19%). Potential denitrification and anammox rates in OY areas were 2.25 and 1.80 times higher than those in NOY areas, respectively (P < 0.01). Redundancy analysis (RDA) identified TOC, SOD, sulfide, Fe[2+], Fe[3+], and NH4[+] as key drivers of these processes. Metagenomic analysis revealed that OY sediments were enriched in Bacillota and Bacteroidota at the phylum level, and key functional genes (nirS, nosZ, hzsB) were significantly more abundant in OY areas (P < 0.05), suggesting enhanced genetic potential for nitrogen removal. The stronger promotion of denitrification over anammox was attributed to the combined effects of TOC (electron donors), Fe[2+] (electron carrier), and sulfide (alternative electron donor for denitrification but inhibitor for anammox). These findings demonstrate that oyster aquaculture enhances the functional capacity for sedimentary nitrogen removal through physicochemical modification, microbial community selection, and enrichment of key functional genes.},
}

@article {pmid42880177,
year = {2026},
author = {Zhong, C and Zhang, J and Wang, Y and Lu, K and Sun, Y and Li, X and Ma, H and Guan, L},
title = {Oudemansiella raphanipes polysaccharide alleviates DSS-induced colitis associated with gut microbiota and ZBP1-associated PANoptosis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158856},
doi = {10.1016/j.phymed.2026.158856},
pmid = {42880177},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease with limited preventive options. The edible mushroom Oudemansiella raphanipes produces polysaccharides with reported bioactivity, but the effects of its purified fraction Oudemansiella raphanipes polysaccharide (UAE-ORP) on colitis remain unknown.

PURPOSE AND METHODS: UAE-ORP was evaluated in mice with sodium dextran sulphate (DSS)-induced colitis using metagenomic and metabolomic analysis, as well as histological, ELISA and Western blot analysis of intestinal barrier function, ZBP1-associated PANoptosis-related proteins, and FFAR2/FFAR3 expression.

RESULTS: UAE-ORP alleviated DSS-induced colonic injury, reducing the DAI scores to 1.7 ± 0.3-2.7 ± 0.5 across treatment groups and restoring colon length to 6.2 ± 0.9-8.2 ± 0.8 cm across doses. UAE-ORP was associated with attenuated ZBP1-associated PANoptosis-related protein expression, increased Lachnospiraceae abundance, and restored acetic acid and 3,4-dihydroxyphthalate levels. UAE-ORP also restored the protein expression levels of FFAR2 and FFAR3. Correlation analysis suggested a potential association between Lachnospiraceae-related metabolites and FFAR2/FFAR3 signaling.

CONCLUSION: UAE-ORP alleviates DSS-induced colitis in mice. The protective effects coincide with altered gut microbiota composition, elevated microbial metabolites, restored FFAR2/FFAR3 expression, and concomitant changes in ZBP1-associated PANoptosis-related protein. These observations identify several candidate pathways warranting further investigation and provide preliminary mechanistic context for the anti-colitic activity of this mushroom polysaccharide.},
}

@article {pmid42880330,
year = {2026},
author = {Forrest-Hammond, R and Kopec, A and Alcolea-Medina, A and Batra, R and Brown, K and Enne, V and Edgeworth, J and Hemingway, J and Hoskote, A and Torres Montaguth, OE and Morfopoulou, S and Peters, M and Robertson, H and Ray, S and Schmidt, A and Snell, LB and Storey, N and Ward, D and De, S and Dixon, G and Hatcher, J and Soothill, J and Breuer, J and Brown, JR},
title = {Implementation of rapid pan-microbial metagenomics in paediatric intensive care: a single-centre, prospective, observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101461},
doi = {10.1016/j.lanmic.2026.101461},
pmid = {42880330},
issn = {2666-5247},
abstract = {BACKGROUND: Few clinical metagenomics studies have reported rapid results with associated clinical impact or described deployment of protocols beyond centres in which they were developed. We aimed to assess the feasibility and clinical impact of implementing a previously validated rapid pan-microbial respiratory metagenomic service in paediatric intensive care, reporting protocol modifications, feasibility, diagnostic performance, clinical impact, and staff perspectives.

METHODS: This single-centre, prospective, observational study was carried out at a general paediatric intensive care unit (ICU) and a cardiac paediatric ICU in Great Ormond Street Hospital (London, UK) between Nov 4, 2024, and Feb 28, 2025. Respiratory samples were obtained from patients selected by intensive care staff based on clinical suspicion of lower respiratory tract infection, with no exclusion criteria. Samples were analysed by a well-established published metagenomic workflow that simultaneously detects bacteria, fungi, and DNA and RNA viruses and provides same-day preliminary results and next-day final results; separate aliquots were sent for concurrent culture and PCR testing. Clinical impact (change in antimicrobials, diagnosis, or infection control) was evaluated through electronic health record review. Clinical staff were surveyed for their feedback via an anonymous online semistructured questionnaire.

FINDINGS: 177 samples from 122 patients (median age 3·4 months [IQR 1·2-36·0]; 54% male) were tested. 174 (98%) samples passed quality control. Sensitivity at 16-h sequencing was 89% (95% CI 80-95) for bacteria, 100% (70-100) for fungi, and 87% (76-93) for viruses, with specificities greater than or equal to 99% across all kingdoms. 42 (24%) of 174 samples analysed by metagenomics yielded 50 organisms that were not detected by routine diagnostics, all of which were confirmed by orthogonal PCR testing. Clinical impact was observed in 51 (29%) of 174 samples, comprising changes in antimicrobial therapy in 46 (26%) samples. Of these 46 samples, 15 (33%) resulted in cessation of antibiotics, ten (22%) in initiation of antibiotics, six (13%) in a change of antibiotic therapy, and 15 (33%) provided confidence to continue an empirical antibiotic choice. Of the 33 ICU staff members surveyed, 23 (72%) reported a positive view of metagenomics, none reported negative views, and 22 (67%) perceived additional benefits over routine testing.

INTERPRETATION: This clinical pilot of rapid respiratory metagenomics in paediatric intensive care showed high specificity and good sensitivity. Protocols developed for an adult population were adapted to a paediatric population, including adaptations for polymicrobial upper respiratory tract samples, which are more common in children. However, increased sensitivity and antimicrobial resistance prediction will be required for broader clinical implementation. Although changes in patient management were observed, particularly for antimicrobial stewardship, delineating the true contribution of metagenomic results offered by this study is difficult. Multicentre studies over multiple winter seasons, with control arms and predefined selection of patients and sample types, are needed to assess the impact on patient outcomes and cost-effectiveness.

FUNDING: NHS Respiratory Metagenomics Network (NHS England).},
}

@article {pmid42880389,
year = {2026},
author = {Yang, Z and Zhang, X and Zheng, S and Huang, Y and Wei, X and Zhang, Y},
title = {Gut Microbiota Remodeling Correlates with Pentose Phosphate Pathway Activation and Steroid Hormone Biosynthesis Dysregulation in Polystyrene Nanoplastic-Induced Hepatic Lipotoxicity.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112378},
doi = {10.1016/j.cbi.2026.112378},
pmid = {42880389},
issn = {1872-7786},
abstract = {Polystyrene nanoplastics (PS-NPs) have been detected in human tissues, but the systemic consequences of chronic oral exposure remain unclear. Female Sprague-Dawley rats received environmentally relevant PS-NP concentrations of 5 or 50 mg/L in drinking water for 42 days. Gut-liver-endocrine interactions were assessed by 16S rRNA sequencing, shotgun metagenomics, fecal metabolomics, hepatic transcriptomics, and biochemical validation of selected nodes. PS-NP exposure caused notable dysregulation of serum and hepatic lipids and produced histopathological damage in the liver. The exposure was also associated with gut dysbiosis dominated by Bacteroidia, along with hepatic glucose-6-phosphate dehydrogenase (G6PD) upregulation and pentose phosphate pathway (PPP) activation, as well as NADPH accumulation. Low-dose exposure was associated with adaptive redox responses (elevated hepatic superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX)) and lipid clearance signatures, whereas high-dose exposure correlated with GSH-PX depletion, elevated 8-iso-prostaglandin (8-iso-PG), and transcriptomic evidence of mitochondrial impairment and ferroptosis vulnerability. Steroid hormone biosynthesis (SHB) disruption-declining estradiol and rising cortisol-was observed across both doses, with ovarian Cyp19a1/Cyp11a1 downregulation at low dose and additional adrenal Cyp21a2 upregulation at high dose. Multi-omics integration linked Bacteroidia enrichment to the PPP intermediate deoxyribose 5-phosphate and to reduced estrogen metabolites. Collectively, these findings outline a Gut Microbiota-PPP-SHB (GMPS) axis as a candidate integrative framework for understanding PS-NP-associated hepatic lipotoxicity. This work offers an integrative resource that identifies candidate pathways and testable hypotheses for future investigation of metabolic risks from chronic nanoplastic exposure.},
}

@article {pmid42880476,
year = {2026},
author = {Li, P and Ge, J and Wang, Y and Han, Y and Zheng, T and Liu, J and Li, L},
title = {Molecular insights into microbial transformation of dissolved organic matter from a wastewater treatment plant.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125936},
doi = {10.1016/j.envres.2026.125936},
pmid = {42880476},
issn = {1096-0953},
abstract = {Dissolved organic matter (DOM) in treated wastewater influences effluent reactivity and ecological risks. How biological treatment configurations reshape DOM at the molecular level remains unclear. This study integrated molecular characterization, metagenomic microbial community analysis and metatranscriptomic functional profiling, machine-learning interpretation, and dynamic Partial Mantel Distance network analysis to compare DOM transformation in full-scale anaerobic-anoxic-oxic process (A2O) and oxidation ditch process (OD). The A2O exhibited a stronger redox-stage-dependent DOM remodeling than the OD. In the A2O, the final aerobic effluent showed a reduced mean molecular weight of 411.45, higher O/C, and lower H/C, with lipid-like and protein-like compounds decreasing from 35.13% to 15.39% and from 35.70% to 21.44%, respectively, whereas the lignin/CRAM-like fractions increased to 47.64%, indicating preferential removal of labile aliphatic and proteinaceous molecules and enrichment of refractory DOM. The OD retained a higher final molecular weight of 451.43 and a lipid-like fraction of 33.94%, suggesting gradual stabilization under continuous circulation and mixed redox microenvironments. The microbial communities differed significantly between the processes, whereas the enzyme profiles showed weaker separation, indicating functional redundancy. The Random Forest models effectively predicted the DOM molecular fate in both processes, with macro AUC values of 0.8913 and 0.8923 for the A2O and OD, respectively. The dPMD networks revealed intermediate-mediated cascade transformations. The treatment configuration governed DOM persistence, microbial ecological control, and the refractory character of the residual effluent DOM. This study provides a molecular-level theoretical basis for optimizing biological wastewater treatment processes, regulating refractory DOM, and reducing the ecological risks associated with treated wastewater discharge.},
}

@article {pmid42880507,
year = {2026},
author = {Shirazi, MMA and Dilorom, O and Baxtiyorovna, SG and Smerat, A},
title = {Zoonotic Viral Spillover: From Reservoir Ecology and Viral Evolution to Pandemic Prevention.},
journal = {Virus research},
volume = {},
number = {},
pages = {199818},
doi = {10.1016/j.virusres.2026.199818},
pmid = {42880507},
issn = {1872-7492},
abstract = {Zoonotic viral spillover represents a major global health challenge arising from complex interactions among viral evolution, reservoir ecology, host biology, environmental disruption, and human activities. Successful emergence requires viruses to overcome successive ecological, cellular, and immunological barriers, including receptor compatibility, cellular tropism, replication efficiency, and innate immune restriction. Reservoir hosts such as bats, rodents, birds, and livestock contribute to viral maintenance and diversification through distinct ecological and physiological characteristics, while deforestation, agricultural expansion, wildlife trade, intensive farming, urbanization, and climate variability can increase opportunities for cross-species transmission. Following spillover, viral adaptation and host susceptibility determine whether infections remain sporadic or progress to sustained human transmission. This review integrates ecological, molecular, immunological, and anthropogenic determinants of zoonotic emergence and examines major historical spillover events involving coronaviruses, influenza viruses, filoviruses, henipaviruses, and arboviruses. We further evaluate genomic and metagenomic surveillance, wastewater monitoring, artificial intelligence, ecological modeling, and integrated One Health approaches for early risk assessment and pandemic preparedness. Major knowledge gaps include limited characterization of global viral diversity, surveillance bias, inadequate functional validation of newly identified viruses, fragmented data systems, and limited predictive capacity. Future prevention requires integration of technological innovation with ecological conservation, equitable surveillance capacity, responsible biotechnology governance, and sustainable One Health Planetary Health strategies.},
}

@article {pmid42880575,
year = {2026},
author = {Li, X and Xue, R and Hu, L and Jiang, Y and Zhu, F and Xiang, C and Jiang, J and Wu, C and Jiang, G and Xue, S},
title = {Coupled and decoupled antimony-arsenic mobility along environmental gradients in a mining soil: Links to geochemical contexts and microbial functional potential.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129334},
doi = {10.1016/j.envpol.2026.129334},
pmid = {42880575},
issn = {1873-6424},
abstract = {Distinct redox behavior, surface-binding affinities, and microbial transformation pathways of antimony (Sb) and arsenic (As) complicate sustainable remediation of mining soils. Understanding how these differences shape field mobility is essential for nature-based remediation that avoids unnecessary inputs. Yet whether natural gradients produce generalizable Sb-As mobility patterns and mechanisms remains unclear. Here, we integrated physicochemical, metagenomic, and statistical analyses to determine how field gradients shaped microbial functional potential and Sb-As mobility at a single Sb smelting site. We identified two Sb-As mobility modes, further supported by external validation across 60 published studies. In the decoupled mode, along resource-driven gradients including moisture, soil organic carbon, and slope-associated light exposure, water-extractable Sb increased whereas As decreased. In the coupled mode, along pH-redox gradients, especially in alkaline and oxic soils, water-extractable Sb and As increased together. The decoupled mode was generally characterized by Sb(V) and As(V) species with Sb redistribution into more labile pools but As retention in stable fractions. Metagenomic profiles linked this decoupling to heterogeneous C-N-S-Fe geochemical contexts that reshaped microbial functional potential related to electron transfer and mineral-associated reactions. By comparison, the coupled mode was characterized by redistribution of Sb and As into reactive fractions under direct pH/Eh control. Hierarchical partitioning identified environmental factors as the dominant explanatory domain for Sb and As (62.5% and 53.1% of adjusted-R[2]-based relative importance), with metagenomic functional variables contributing 18.5% and 9.3%, respectively. These contrasting mobility modes help distinguish when Sb and As may require joint or separate management, thereby supporting targeted nature-based remediation.},
}

@article {pmid42880576,
year = {2026},
author = {Liu, J and Chen, S and Huang, J and Lin, D and Zhang, L},
title = {Size-dependent Effects of Polystyrene Micro- and Nanoplastics on Gastrointestinal Microbiota in Mice: Overlooked Axial Site-Specific Heterogeneity and Radial Mucosal-Luminal Compartment Divergence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129351},
doi = {10.1016/j.envpol.2026.129351},
pmid = {42880576},
issn = {1873-6424},
abstract = {Accumulating evidence links micro- and nanoplastics (MNPs) exposure to gastrointestinal (GI) health impairment, especially via gut microbiota disruption. However, most studies focus on fecal or cecal luminal microbiota, neglecting the inherent spatial heterogeneity of the GI tract and distinct mucosal versus luminal microbial niche responses. In this study, multi-omics was applied to investigate the effects of polystyrene nanoplastics (PS-NPs, 100 nm) and microplastics (PS-MPs, 5 μm) on mouse GI microbiota following 4-week drinking water exposure. 16S rDNA sequencing revealed that MNPs altered mucosal microbiota across the stomach, jejunum, and cecum in a size- and site-specific manner: PS-MPs predominantly disrupted gastric mucosal communities, while PS-NPs dominated perturbations in the jejunal and cecal mucosa. Correlation analysis showed that these microbial dysbioses were significantly associated with hepatorenal functional impairment, as evidenced by elevated serum γ-glutamyl transferase, alanine aminotransferase, and lactate dehydrogenase activities. Strikingly, metagenomic sequencing showed that, in stark contrast to mucosal microbiota, PS-MPs exerted more pronounced effects on the structural and functional profiles of cecal luminal microbiota than PS-NPs. Consistently, untargeted metabolomics identified more differential metabolites in cecal contents of PS-MPs-exposed mice (288) than PS-NPs-exposed counterparts (213). Our results demonstrate that microbial niche heterogeneity and size-dependent effects are critical determinants of MNP gastrointestinal toxicity, which must be incorporated into health risk assessment to guide evidence-based pollution management.},
}

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42881180,
year = {2026},
author = {Anjur-Dietrich, MI and Jones, KG and Mullet, JI and Vo, NN and Castro, KG and Parker, SM and Chisholm, SW},
title = {Biofilm formation and dynamics in the marine cyanobacterium Prochlorococcus.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881180},
issn = {2041-1723},
support = {984601//Simons Foundation/ ; },
mesh = {*Prochlorococcus/physiology/genetics/growth & development/metabolism ; *Biofilms/growth & development ; Seawater/microbiology ; Carbon/metabolism ; Photosynthesis ; },
abstract = {The picocyanobacterium Prochlorococcus is responsible for ~10% of annual marine carbon fixation and plays a role in the global carbon budget. While these phototrophs are primarily considered free-living and neutrally buoyant in the euphotic zone, we observe that they can form biofilms on diverse substrates. This trait is conserved across Prochlorococcus ecotypes, and populations continuously transition between planktonic and biofilm states via a non-genetic heritable mechanism. Throughout their growth, cells in biofilms retain a reversible, dynamic attachment state, and measurements of growth, photosynthesis, and carbon exudation rates reveal that cells in biofilms exude more organic carbon than their planktonic counterparts. Estimates of the fraction of Prochlorococcus cells attached to particles in the ocean-obtained through metagenomic analysis of serially-fractionated samples-reveal that a significant adherent population exists throughout the euphotic and mesopelagic zones. This work describes a dimension of Prochlorococcus's ecological niche and suggests a role in carbon export to the deep sea.},
}

*Prochlorococcus/physiology/genetics/growth & development/metabolism
*Biofilms/growth & development
Seawater/microbiology
Carbon/metabolism
Photosynthesis

@article {pmid42882385,
year = {2026},
author = {Zhang, X and He, J and Zhai, Z and Zhaoyifan, X and Pei, X and Li, Y and Hou, M},
title = {Tropheryma whipplei as the Dominant Organism in Bronchoalveolar-Lavage Metagenomic Next-Generation Sequencing: A Single-Centre Case Series of 28 Patients.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/diagnostics16193230},
pmid = {42882385},
issn = {2075-4418},
support = {TJSQNYXXR-D2-119//Tianjin Municipal Commission of Health/ ; },
abstract = {Background/Objectives: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) increasingly reports Tropheryma whipplei (T. whipplei) in patients without classical Whipple disease, but the significance of these detections is often uncertain. We aimed to quantify relative sequencing abundance, characterise the accompanying clinical, radiological, and routine laboratory phenotype, and develop a structured framework for interpretation. Methods: We retrospectively reviewed 944 consecutive BALF-mNGS tests performed at Tianjin Chest Hospital between October 2022 and March 2026. T. whipplei was detected in 47 tests; the primary analytic cohort comprised the 28 patients in whom it was the most abundant detected microorganism. Demographics, comorbidities, symptoms, chest computed tomography findings, co-detected organisms, species-level read counts, and routine laboratory indicators were summarised descriptively. Results: T. whipplei was detected in 47/944 tests (4.98%) and was the predominant (most abundant) detected microorganism in 28/47 (59.6%). In these 28 patients, the mean age was 60.2 ± 12.3 years and 15 (53.6%) were women. Cough (18/28, 64.3%) and expectoration (14/28, 50.0%) predominated, whereas fever occurred in 4/28 (14.3%); pulmonary nodules were the most common CT finding (15/28, 53.6%). T. whipplei was the sole microorganism in 11/28 (39.3%) and was co-detected in 17/28 (60.7%); it was sole or ≥10-fold more abundant than the strongest co-detected organism in 25/28 (89.3%). Leukocyte counts were within reference in 26/28, C-reactive protein was ≤5 mg/L in 19/25, and procalcitonin was at or below the assay limit in 12/14. Conclusions: Predominant (most-abundant) BALF-mNGS detection of T. whipplei commonly accompanied nonspecific respiratory presentations and a relatively indolent laboratory phenotype. Because sequence dominance cannot by itself distinguish infection from heavy carriage, interpretation should integrate read burden, orthogonal confirmation, competing pathogens and diagnoses, and systemic features.},
}

@article {pmid42882956,
year = {2026},
author = {Aksomaitiene, J and Novoslavskij, A and Kasparaviciene, B and Malakauskiene, S and Sinkevicius, R and Serniene, L},
title = {Feeder- and Drinker-Associated Microbiota Differ from Host-Associated Fecal Microbiota During a Commercial Broiler Production Cycle with Age-Associated Changes in Taxonomic Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16192987},
pmid = {42882956},
issn = {2076-2615},
support = {No. 963864//Research Council of Lithuania/ ; },
abstract = {Broiler chickens are continuously exposed to microorganisms in the production environment, but the relationship between microorganisms on bird-contact surfaces and fecal microbiota remains unclear. In this exploratory observational study, shotgun metagenomic sequencing was used to compare microbial communities in feeder- and drinker-associated surface samples and individual fecal samples during one production cycle in a single commercial system housing Ross 308 broilers. The dataset comprised 22 individual fecal samples collected on days 1, 7, 19, 27, and 39 and four composite feeder- or drinker-associated environmental surface samples collected on days 1, 19, 27, and 39. Taxonomic composition, alpha and beta diversity, differential taxonomic signatures, and genus-level co-abundance patterns were evaluated. Environmental samples had greater richness and were dominated by Proteobacteria and Bacteroidetes, whereas host-associated fecal samples were dominated by Firmicutes and lactobacilli. Sample type explained 20.0% of variation in Bray-Curtis distances and 15.5% in Binary Jaccard distances (both p = 0.001). Within host-associated samples, Firmicutes increased from 51.4% on day 1 to 93.6% on day 39, while Proteobacteria decreased from 26.5% to 1.4%. Despite these taxonomic changes, host-associated communities did not form statistically distinct clusters by sampling day. Within the investigated production system, host-associated fecal microbial communities differed from those detected on the sampled feeder and drinker surfaces, while the relative abundance of dominant fecal taxa varied across sampling days. These findings are specific to the investigated production system and production cycle.},
}

@article {pmid42882996,
year = {2026},
author = {Shao, KY and Han, F and Chen, PH and Zhu, HB and Liu, BR and Xu, M and Liu, LL},
title = {Effects of Dietary Digestible Energy Levels on Milk Performance, Rumen Fermentation, and Rumen Microbiota in Lactating Bactrian Camels from Southern Xinjiang.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193027},
pmid = {42882996},
issn = {2076-2615},
support = {XJARS-11//Xinjiang Uygur Autonomous Region Dairy Industry Technology System/ ; },
abstract = {This study aimed to investigate the effects of different dietary digestible energy (DE) levels on lactation performance, rumen fermentation, and rumen microbiota in lactating Bactrian camels in southern Xinjiang. Twenty-four mid-lactation Bactrian camels were randomly assigned to four groups, with six camels per group, and were fed diets containing DE levels of 12.25 (CK), 12.49 (LE), 12.74 (ME), and 12.99 MJ/kg (HE), respectively. The experiment lasted 60 days, including a 15-day adaptation period and a 45-day experimental period. Metagenomic sequencing was performed to characterize the composition and functional gene profiles of the rumen microbiota. The results showed that increasing dietary DE significantly increased milk yield, milk fat yield, and lactose yield (p < 0.05), while decreasing ruminal NH3-N concentration. Propionate and butyrate concentrations were significantly higher in the HE group (p < 0.05). No significant differences were detected in rumen pH or the concentrations of acetate, valerate, and total volatile fatty acids among treatments (p > 0.05). No significant differences were detected in rumen microbial α-diversity or overall community structure among dietary DE treatments, although several bacterial genera showed differential enrichment. No significant differences were detected in the relative abundances of genes assigned to the major KEGG pathways or CAZy families among dietary treatments. In conclusion, within the dietary range examined in this study, higher DE was associated with greater lactation performance and changes in rumen fermentation, while no significant differences were detected in the overall rumen microbial community structure or the relative abundances of genes assigned to the major KEGG pathways and CAZy families.},
}

@article {pmid42883021,
year = {2026},
author = {Bao, J and Li, H and Jiang, K and Xu, J and Wu, Y and Ji, W and Li, S and Qi, B and Niu, H},
title = {Comparative Study on Growth Performance and Rumen Digestive Metabolism Between Cull Beef Cows and Fattening Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193052},
pmid = {42883021},
issn = {2076-2615},
support = {(32460813)//National Natural Science Foundation of China/ ; (2025YFDZ0123, 2025ZY0111, YZ2023010, TL20205TW004)//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; (GXKY26Z082).//Inner Mongolia University for Nationalities/ ; },
abstract = {Culled beef cows may retain practical value for fattening after reproductive use, but the rumen and host physiological characteristics associated with this response remain incompletely characterized. This study compared culled beef cows (CBC; n = 9) with fattening bulls (CON; n = 9) using 18 healthy Simmental crossbred cattle fed the same experimental total mixed ration (TMR) under identical feedlot conditions. Growth performance, body condition score (BCS), apparent nutrient digestibility, economic outcomes, blood indices, rumen fermentation, ruminal enzyme activities, rumen metagenomes, and plasma untargeted metabolomes were assessed. Compared with CON, CBC had higher final body weight, average daily gain, feed intake, and apparent digestibility of dry matter, crude protein, and neutral detergent fiber, whereas the feed-to-gain ratio did not differ significantly between groups (p = 0.692). BCS increased significantly from day 0 to day 60 within both cattle categories. Because different, non-cross-calibrated BCS reference frameworks were used, no between-group comparison of BCS was made. Economic analysis indicated that the value attributable to actual live-weight gain was similar between groups when within-category prices were held constant, whereas the relative economic outcome varied with feed costs and changes in live-cattle market prices. CBC also showed more propionate-oriented fermentation, greater fibrolytic enzyme activities, distinct carbohydrate-active enzyme profiles, higher insulin and leptin, and lower non-esterified fatty acids and β-hydroxybutyrate. Because lean and fat mass were not directly measured, the tissue basis of the greater weight gain remains unresolved. Overall, CBC exhibited a stronger fattening response accompanied by coordinated differences in rumen function and host metabolic profiles.},
}

@article {pmid42883035,
year = {2026},
author = {Shahbaz, GM and Ashraf, Z and Chen, S and Wang, C and He, C and Sun, H and Zhu, L and Liu, L and Wang, M and Wu, L and Gu, R and Li, W and Xing, F},
title = {Emerging and Novel Ovine Viruses: Molecular Diagnostics, Genomic and Metagenomic Surveillance, and One Health Perspectives.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193066},
pmid = {42883035},
issn = {2076-2615},
support = {No. U25A20699//Joint Funds of the National Natural Science Foundation of China/ ; No. TDZKCX202401//President's Fund Project of Tarim University/ ; No. 2024A02004-3//the Major Science and Technology Special Project of Xinjiang Uygur Autonomous Region/ ; No. BTYJXM-2024-S23//the Postgraduate Practical Innovation Project of Xinjiang Production and Construction Corps/ ; },
abstract = {Emerging and novel ovine viruses pose increasing threats to animal health, livestock productivity, trade, food security, and public health preparedness. Their emergence is driven by complex interactions among animal movement, mixed-species production systems, wildlife-livestock interfaces, arthropod vectors, environmental changes, and viral evolution. This review critically compares current strategies for identifying major, emerging, re-emerging, zoonotic, and newly recognized ovine viruses, with emphasis on their analytical sensitivity, turnaround time, throughput, operational cost, accessibility, field applicability, validation status, and capacity for novel-virus detection. Conventional diagnostic approaches, including virus isolation, serology, antigen detection, histopathology, and immunohistochemistry, remain essential for confirmation and flock-level surveillance but may be limited by slow turnaround, dependence on specialized facilities, reduced sensitivity at low viral loads, and an inability to identify highly divergent or unknown viruses. Targeted molecular assays, including PCR, RT-PCR, qPCR, multiplex assays, digital PCR, isothermal amplification, and CRISPR-based diagnostics, have improved detection speed and sensitivity but generally require prior knowledge of viral genomic targets. Genomic and metagenomic approaches, including whole-genome sequencing, next-generation sequencing, nanopore sequencing, viral metagenomics, bioinformatics, and phylogenetic analysis, provide broader detection capabilities by enabling characterization of viral diversity, outbreak tracing, co-infection identification, and discovery of previously unrecognized viruses. However, their interpretation remains challenging due to low viral abundance, poor sample quality, host nucleic acid background, contamination, incomplete reference databases, limited computational capacity, and the inability of sequence detection alone to confirm disease causality. Therefore, future ovine virus surveillance requires integration of molecular diagnostics with active, passive, outbreak-based, risk-based, vector, wildlife, and animal-movement surveillance within a One Health framework. Linking genomic information with ecological, epidemiological, and environmental data will be essential for transforming ovine virus surveillance from reactive diagnosis toward proactive preparedness. Advances in standardized sampling, validated field diagnostics, affordable sequencing, curated databases, bioinformatics capacity, and cross-sector data sharing will strengthen early recognition, risk assessment, and preparedness against emerging viral threats in sheep.},
}

@article {pmid42883377,
year = {2026},
author = {Kakimova, AB and Zaparina, YG and Zayadan, BK and Sandybayeva, SK and Kelden, D and Dauletova, AA and Piazza, S},
title = {Comparative Shotgun Metagenomics of Microbial Communities Associated with Two Geothermal Systems in Kazakhstan.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191704},
pmid = {42883377},
issn = {2079-7737},
support = {АР26194471//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Geothermal-associated microbial communities remain poorly characterized in Central Asia. Here, shotgun metagenomics was used to compare microbial communities associated with thermally influenced substrates from the Chundzha and Rakhman geothermal systems in Kazakhstan. Six metagenomes representing three spatial replicates per site yielded approximately 6.5-7.3 Gb of clean sequence data per sample. Species-level richness showed a directional trend toward higher values in Chundzha, whereas Shannon diversity was similar between sites. Genus-level Bray-Curtis ordination showed apparent site-associated separation, with sampling site explaining 87.3% of the variation, although the effect was not statistically significant (PERMANOVA, R[2] = 0.873, p = 0.10). Chundzha showed greater relative representation of several halophilic and halotolerant taxa, whereas Rakhman showed greater representation of soil-associated lineages. Broad COG and KEGG functional profiles were largely shared between sites. Several hydrogenase-, nitrogenase-, and RuBisCO-associated genes showed higher relative representation in Rakhman, whereas selected fermentation- and photosynthesis-associated functions were relatively higher in Chundzha; however, none of the targeted KO comparisons remained significant after FDR correction. These results indicate candidate taxonomic and functional patterns that should be regarded as exploratory because of the limited replication. The dataset provides a baseline for future genome-resolved and metatranscriptomic studies of geothermal-associated microbial communities in Kazakhstan.},
}

@article {pmid42883560,
year = {2026},
author = {Tong, T and Wu, J and Jia, S and Liao, C and Zhang, H and Xie, J and Chen, W and Huang, Y and Wang, X and Wu, X and Zhou, Y and He, Y and Zhao, K},
title = {Polyphenol Bioconversion and Volatile Aroma Production by Meyerozyma sp. C3 Isolated from Kombucha in the Theaflavin-Sucrose Fermentation Model.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193453},
pmid = {42883560},
issn = {2304-8158},
abstract = {This study integrated metagenomic and untargeted metabolomics analysis to characterize differences in kombucha communities and metabolites between black tea-sucrose and theaflavin-sucrose systems. Theaflavins selectively enriched yeasts, particularly Meyerozyma and Lodderomyces, and increased the annotated abundance of carbohydrate-metabolism genes, glycoside hydrolases, and glycosyltransferases. Based on these community-level findings, the newly isolated Meyerozyma sp. C3 was employed to establish a simplified single-strain fermentation model to investigate the biotransformation potential of the enriched yeast taxon. The strain exhibited stable growth and sustained acidification throughout fermentation, with a theaflavin conversion rate of 39.5% after 7 days. Metabolomic analysis revealed substantial changes in oligosaccharides (e.g., maltotriose, raffinose), flavonoids/flavanes (e.g., epigallocatechin gallate, (+)-gallocatechin, (-)-epigallocatechin, and catechin derivatives), and organic acids (e.g., citric and isocitric acid), while volatile profiling identified 2-phenylethanol and 4-ethylphenol as newly dominant aroma compounds after fermentation. These results indicate that a yeast-driven route for theaflavin transformation and flavor formation, supporting targeted strain mining and functional fermented-tea development.},
}

@article {pmid42883692,
year = {2026},
author = {Zhang, W and Zhu, Y and Chu, X and Zhang, X and Pan, Z and Li, A},
title = {Co-Enrichment of Desulfovibrio and Erysipelotrichaceae and Dysregulation of Multiple Amino Acid Pathways in HFpEF: Insights into TXG-Associated Metabolic Changes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198445},
pmid = {42883692},
issn = {1422-0067},
support = {82174080//National Natural Science Foundation of China/ ; H2022423333//Hebei Provincial Department of Science and Technology/ ; },
mesh = {Animals ; *Amino Acids/metabolism/blood ; *Heart Failure/metabolism/microbiology/drug therapy ; *Desulfovibrio/genetics/isolation & purification ; Mice ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Male ; *Eubacteriales/genetics ; Diet, High-Fat/adverse effects ; Metabolome ; Metagenomics ; },
abstract = {Gut enrichment of Desulfovibrio and Erysipelotrichaceae may be associated with systemic amino acid metabolic dysfunction, myocardial injury, and heart failure with preserved ejection fraction (HFpEF). These taxa appear to influence host amino acid metabolism through distinct processes, but the functional implications of their co-enrichment in HFpEF remain unclear. Total xanthones from Gentianella acuta (TXG) have documented cardioprotective effects, although their effects on gut microbiota and systemic metabolism remain unexplored. We established a mouse model of HFpEF using a high-fat diet (HFD) combined with Nω-nitro-L-arginine methyl ester (L-NAME). We integrated 16S rRNA sequencing, fecal metagenomics, and targeted serum amino acid metabolomics to examine microbe-metabolite associations, with echocardiography and histopathology providing complementary phenotypic evidence. Microbial and metabolomic analyses revealed pronounced enrichment of Desulfovibrio and Erysipelotrichaceae (particularly Dubosiella), accompanied by elevated serum isoleucine, tryptophan, and homocysteine levels. TXG treatment was associated with lower abundance of both taxa, altered serum amino acid profiles, preserved colonic barrier integrity, and reduced myocardial inflammation and fibrosis. These changes coincided with improved diastolic function. Together, these findings associate co-enrichment of the two taxa with dysregulation of multiple amino acid pathways in HFpEF. TXG treatment was accompanied by attenuated cardiac and metabolic injury as well as shifts in gut-microbiota profiles, with these correlative observations motivating further investigation of Gentianella acuta for metabolic heart failure.},
}

Animals
*Amino Acids/metabolism/blood
*Heart Failure/metabolism/microbiology/drug therapy
*Desulfovibrio/genetics/isolation & purification
Mice
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Male
*Eubacteriales/genetics
Diet, High-Fat/adverse effects
Metabolome
Metagenomics

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods

@article {pmid42883729,
year = {2026},
author = {Liu, N and Zhang, S and Li, Y},
title = {Molecular Mechanisms of the Gut-Liver-Placenta Axis in Intrahepatic Cholestasis of Pregnancy: Microbiota-Associated Pathogenesis and Next-Generation Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198481},
pmid = {42883729},
issn = {1422-0067},
support = {XLYC2412033//LiaoNing Revitalization Talents Program/ ; },
mesh = {Humans ; Female ; *Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology ; Pregnancy ; *Pregnancy Complications/metabolism/microbiology/therapy/etiology ; *Placenta/metabolism ; Bile Acids and Salts/metabolism ; Animals ; *Liver/metabolism/pathology ; *Gastrointestinal Microbiome ; Dysbiosis ; },
abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder characterized by elevated maternal bile acid concentrations and an increased risk of adverse perinatal outcomes. Genetic susceptibility, hormonal changes, and impaired bile acid transport contribute to its development but do not fully explain the variability in disease severity and fetal outcomes. Increasing evidence suggests that gut microbiota dysbiosis and altered bile acid metabolism are associated with ICP and may participate in disease development through the gut-liver-placenta axis. In this review, we integrate evidence on bile acid-microbiota interactions during pregnancy, ICP-associated microbial and metabolic alterations, and their possible links to placental and fetal outcomes. Human studies primarily support associations among microbial alterations, bile acid profiles, and disease severity, whereas the microbiota-mediated effects on placental function and fetal injury proposed to date are supported largely by experimental models. We further discuss potential links among gut microbial dysfunction, placental oxidative stress, fetal cardiac injury, neurodevelopmental risk, offspring metabolic susceptibility, and iatrogenic prematurity. Although ursodeoxycholic acid (UDCA) improves maternal pruritus and selected biochemical indices, its effect on major perinatal outcomes remains uncertain. Ileal bile acid transporter (IBAT) inhibitors and microbiota-targeted interventions remain investigational, with insufficient pregnancy-specific evidence regarding their efficacy and maternal-fetal safety. Future studies should clarify the associated causal mechanisms and integrate metagenomic, metabolomic, and placental data to identify clinically relevant biomarkers and therapeutic targets.},
}

Humans
Female
*Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology
Pregnancy
*Pregnancy Complications/metabolism/microbiology/therapy/etiology
*Placenta/metabolism
Bile Acids and Salts/metabolism
Animals
*Liver/metabolism/pathology
*Gastrointestinal Microbiome
Dysbiosis

@article {pmid42883733,
year = {2026},
author = {Abdulkhakov, SR and Safina, DD and Markelova, MI and Ponomareva, ER and Siniagina, MN and Khusnutdinova, DR and Kupriyanova, OV and Abdulkhakov, RA and Grigoryeva, TV},
title = {Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198485},
pmid = {42883733},
issn = {1422-0067},
support = {12/2025-PD-KFU//Tatarstan Academy of Sciences/ ; },
mesh = {Humans ; *Inulin/pharmacology/therapeutic use/administration & dosage ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/metabolism ; Adult ; *Butyric Acid/pharmacology/therapeutic use/administration & dosage ; Middle Aged ; Metagenomics/methods ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Female ; Male ; Fatty Acids, Volatile/metabolism ; Metabolomics/methods ; *Metabolome ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; Metagenome ; },
abstract = {The long-term impact of eradication therapy for Helicobacter pylori on the gut microbiota is a subject of significant interest. To evaluate the influence of the bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin on functional alterations within the gut microbial community, metagenomic and metabolomic profiling were performed. Fecal samples were collected from 15 patients (aged 19-64 years) prior to the treatment, immediately after the treatment, and one month after the therapy. A significant decrease in the relative abundance of Actinobacteria, such as Bifidobacterium and Collinsella, was observed after the therapeutic intervention. In contrast, the levels of Faecalibacterium prausnitzii remained consistent, while Roseburia faecis levels exhibited a substantial decline, suggesting a disruption in key butyrate-producing bacteria. A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed. A comprehensive analysis of short-chain fatty acids (SCFAs) levels in the feces of the patients revealed a decline in the butyric acid concentration in response to the therapy, followed by a return to baseline levels. However, the level of valeric acid declined, and there was no tendency for it to increase after a month-long course of therapy. It is important to note that these shifts persisted for a period of four weeks. Consequently, the H. pylori eradication therapy intervention promotes a persistent microbial reorganization, and the observed recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation. To confirm the conclusions, a larger sample size and longer-duration studies are required.},
}

Humans
*Inulin/pharmacology/therapeutic use/administration & dosage
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/metabolism
Adult
*Butyric Acid/pharmacology/therapeutic use/administration & dosage
Middle Aged
Metagenomics/methods
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Female
Male
Fatty Acids, Volatile/metabolism
Metabolomics/methods
*Metabolome
Young Adult
Anti-Bacterial Agents/therapeutic use
Metagenome

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198493},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42883855,
year = {2026},
author = {Dessalegn, B and Debelo, M and Palmieri, N and Dublecz, K and Hess, M and Awad, WA},
title = {Early-Life Oat Supplementation Is Associated with Altered Cecal Microbiota and Microbial Metabolic Profiles and Reduced Campylobacter jejuni Colonization in Broiler Chickens.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198607},
pmid = {42883855},
issn = {1422-0067},
support = {FWF; P 36720//FWF Austrian Science Fund/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology/metabolism ; *Campylobacter jejuni ; *Avena/chemistry ; *Dietary Supplements ; *Campylobacter Infections/veterinary/microbiology ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Amino Acids/metabolism ; Fatty Acids, Volatile/metabolism ; Diet ; *Metabolome ; *Poultry Diseases/microbiology/prevention & control ; },
abstract = {Campylobacter jejuni is a leading foodborne pathogen that commonly colonizes the intestinal tract of broiler chickens and represents a significant food safety concern. Dietary intervention may provide a practical approach to modulate the gut microbiota and reduce pathogen colonization. This study investigated the effects of oat supplementation on C. jejuni colonization and dissemination, cecal microbiota and predicted functions, and cecal short-chain fatty acids (SCFAs) and ileal amino acid profiles during early-life infection in broiler chickens. One-day-old Ross 308 broiler chickens were fed a basal diet or diets containing 10% oat (MDF) or 20% oat (HDF) and orally infected with C. jejuni at 2 days of age. C. jejuni loads in the cecum, jejunum, liver, and spleen were quantified by culture. Cecal microbiota composition and predicted functional profiles were characterized by shotgun metagenomic sequencing, while cecal SCFAs and ileal amino acids were quantified at 21 and 35 dpi using gas chromatography and an automatic amino acid analyzer, respectively. Oat supplementation reduced intestinal C. jejuni loads and limited dissemination to the liver and spleen, with the MDF diet reducing cecal loads by up to 3.3 log10 CFU/g at 35 dpi (p < 0.05). Infection altered cecal microbial diversity and community structure, while oat supplementation modified these infection-associated microbial patterns, with MDF showing the most consistent effects. Differential abundance analysis identified changes in taxa, including Bacteroides, Parabacteroides, and Phocaeicola, together with changes in predicted functions related to motility and chemotaxis, iron acquisition, and dormancy/sporulation. These microbial changes coincided with alterations in cecal isobutyrate and ileal amino acids, particularly glutamate, serine, proline, and aspartate, in MDF-fed infected chickens. Overall, MDF supplementation was most consistently associated with reduced C. jejuni colonization and dissemination and concurrent changes in the developing cecal microbial and metabolic profiles.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology/metabolism
*Campylobacter jejuni
*Avena/chemistry
*Dietary Supplements
*Campylobacter Infections/veterinary/microbiology
Animal Feed
*Gastrointestinal Microbiome/drug effects
Amino Acids/metabolism
Fatty Acids, Volatile/metabolism
Diet
*Metabolome
*Poultry Diseases/microbiology/prevention & control

@article {pmid42884044,
year = {2026},
author = {Ravin, NV and Gureeva, MV and Beletsky, AV and Grabovich, MY},
title = {The Genomic Characterization of a Novel Candidatus Genus of the Family Gallionellaceae, a Novel Candidatus Species of the Genus Gallionella and Their Metabolic Potential for Iron Oxidation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198801},
pmid = {42884044},
issn = {1422-0067},
support = {25-14-00062//Russian Science Foundation/ ; },
mesh = {Oxidation-Reduction ; *Iron/metabolism ; Phylogeny ; *Genome, Bacterial ; *Gallionellaceae/genetics/metabolism/classification ; Genomics/methods ; },
abstract = {The family Gallionellaceae includes neutrophilic, aerobic, iron-oxidizing bacteria, many of which remain uncultured and known only from metagenomic data. In this study, two high-quality Gallionellaceae genomes were assembled from a ferruginous spring in the Voronezh region, Russia. Phylogenetic analysis based on 120 concatenated proteins, ANI (average nucleotide identity), and AAI (average amino acid identity) indicates that BG-057 belongs to the genus Gallionella and BG-364 to the genus 39-52-133. We propose the names "Candidatus Gallionella aquifuscii" sp. nov. for BG-057 and "Candidatus Dubininella ochracea" gen. nov., sp. nov. for BG-364. Both genomes encode genes for the Calvin-Benson-Bassham (CBB) cycle. Both are potentially capable of aerobic respiration due to the presence of electron transfer chain components. Both genomes encode the iron oxidase Cyc2, and BG-057 also encodes MtoA. BG-057 is potentially capable of lithotrophic growth in the presence of H2 and H2S. BG-364 is potentially capable of growth via Mn (II) oxidation; arsenite oxidation; the direct oxidation of thiosulfate; H2S, elemental sulfur, and sulfite oxidation. BG-364 encodes denitrification genes (narGHI, nirS, norBC). BG-057 possesses systems for the biosynthesis and export of siderophores, while BG-364 lacks these systems but retains Ton-dependent receptors, suggesting the use of exogenous siderophores.},
}

Oxidation-Reduction
*Iron/metabolism
Phylogeny
*Genome, Bacterial
*Gallionellaceae/genetics/metabolism/classification
Genomics/methods

@article {pmid42884152,
year = {2026},
author = {Jenkins Sánchez, L and Poppe, J and Baudot, A and Vu, LD and Villella, W and Van den Abbeele, P},
title = {Impact of Triacetin- and Tributyrin-Based Formulations on IBS Microbiome Composition and SCFA Profiles: A Preclinical Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198910},
pmid = {42884152},
issn = {1422-0067},
mesh = {Humans ; *Triglycerides/pharmacology ; *Fatty Acids, Volatile/metabolism ; *Triacetin/pharmacology ; *Irritable Bowel Syndrome/microbiology/drug therapy/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Adult ; Male ; Prebiotics/administration & dosage ; Female ; Butyrates/metabolism ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent yet poorly understood functional gut disorder frequently associated with microbial dysbiosis, making microbiome-targeting interventions a promising management strategy. In this study, we evaluated the microbiome-modulating potential of three doses of triacetin (TA; ReBiome™; 100, 200 and 300 mg/day) and two finished formulations containing TA and/or tributyrin (TB): Active Biome™ (AB) and Bio Complete 3™ (BC3). Inulin served as a benchmark prebiotic. The validated ex vivo Systemic Intestinal Fermentation Research (SIFR[®]) technology pipeline was applied using fecal microbiota from eight adults with IBS. TA dose-dependently increased short-chain fatty acid (SCFA) levels from 100 mg/day, significantly increasing acetate and butyrate while maintaining low gas formation. In addition to acetate and butyrate, AB and BC3 also promoted propionate while BC3 induced a particularly pronounced butyrate increase. Overall, both formulations induced stronger SCFA but milder gas increases than inulin. TA, AB and BC3 enriched IBS-depleted, butyrate-associated OTUs related to Faecalibacterium and Anaerobutyricum species. AB and BC3 increased microbial diversity (community modulation score (CMS)) by promoting Bifidobacteriaceae, Lachnospiraceae and Bacteroidaceae. Overall, TA and TA/TB-containing formulations promoted butyrate production, potentially helping mitigate IBS symptom severity by inducing a favorable fermentation profile with limited gas formation.},
}

Humans
*Triglycerides/pharmacology
*Fatty Acids, Volatile/metabolism
*Triacetin/pharmacology
*Irritable Bowel Syndrome/microbiology/drug therapy/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Fermentation
Adult
Male
Prebiotics/administration & dosage
Female
Butyrates/metabolism

@article {pmid42884177,
year = {2026},
author = {Rodríguez-Costas, N and Rodríguez-Blanco, A and Expósito, CR and Cubiella, J and Stompel, ES and Fernández-de-Ana Portela, C and Martín, AID and Taboada-Rodríguez, P and Silva, BF and Fernández, MDR and Zarraquiños, S and Remedios, D and Gómez, CAS and Lorenzo, SA and Poceiro, RF and Parga, MLC and Ramírez, VH and Pérez-Castro, S},
title = {Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198936},
pmid = {42884177},
issn = {1422-0067},
support = {N.º Solicitud SOL-00105490, N.º Expediente EXP0010549//Centre for Industrial Technological Development/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Fungi/chemistry ; Female ; Male ; Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Aged ; },
abstract = {The gut microbiome is increasingly recognized as an important determinant of host immune regulation, intestinal homeostasis, and recovery after colorectal cancer (CRC) surgery. Although our previous randomized, double-blind, placebo-controlled clinical trial demonstrated that fungal nutraceutical supplementation with Micodigest[®] was associated with favorable taxonomic and systemic inflammatory changes in patients undergoing CRC surgery with curative intent, the functional consequences of this intervention remain poorly understood. Here, we performed a functional metagenomic analysis of fecal samples collected from patients enrolled in the original clinical trial to investigate whether Micodigest[®] supplementation was associated with changes in the functional potential of the gut microbiome. A total of 37 patients were analyzed, including 24 receiving Micodigest[®] and 13 receiving placebo, with paired samples collected before supplementation and after 4-6 weeks of intervention. Shallow shotgun metagenomic sequencing was performed, and microbial functional potential was characterized using KEGG Orthologues (KOs). Differential abundance analysis identified 14 significantly different KOs between groups at baseline and 23 after intervention, with no overlap between the two sets of orthologues. Following supplementation, Micodigest[®]-treated patients exhibited increased representation of functions related to CRISPR-associated systems, bacteriophage biology, and chitin-derived carbohydrate utilization, together with reduced representation of nutrient acquisition systems, conjugative transfer, sulfur metabolism, and components of the Wood-Ljungdahl pathway. These functional signatures suggest coordinated changes in microbial ecological adaptation, nutrient utilization, genetic exchange, and metabolic activity following fungal nutraceutical supplementation. Integration with previously reported taxonomic and inflammatory findings supports the hypothesis that Micodigest[®] may promote coordinated remodeling of the gut microbiome and host-microbiota interactions during the perioperative period. Although the present study cannot establish causality or directly infer microbial activity from metagenomic potential, these findings provide novel functional insights into the microbiome response to fungal nutraceutical supplementation in patients with CRC and highlight functional metagenomics as a valuable complement to taxonomic profiling.},
}

Humans
*Colorectal Neoplasms/microbiology
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Fungi/chemistry
Female
Male
Feces/microbiology
Metagenomics/methods
Middle Aged
Aged

@article {pmid42884562,
year = {2026},
author = {Xu, Z and Lau, RI and Qi, H and Wong, MCS and Chan, KHN and Lau, ISF and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {Synbiotic HQP08 Supplementation for Hair Loss and Depressive Symptoms: An Open-Label Pilot Study of Clinical Outcomes and Gut Microbiome Changes.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193111},
pmid = {42884562},
issn = {2072-6643},
support = {//InnoHK/ ; },
mesh = {Humans ; Pilot Projects ; *Alopecia/microbiology/therapy ; Female ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Synbiotics/administration & dosage ; Treatment Outcome ; *Depression/therapy/microbiology ; *Bifidobacterium longum ; Dietary Supplements ; Young Adult ; },
abstract = {Background: Gut microbiota dysregulation has been implicated in hair loss via the gut-skin axis, but human interventional data are limited. We previously showed that Bifidobacterium longum HK003 reverses alopecia-like phenotypes in mice. Methods: We conducted an open-label, single-arm pilot study to evaluate an HK003-containing synbiotic (HQP08) in 32 adults with self-reported hair loss over 8 weeks. The primary endpoint was the proportion of participants reporting improvement on the Patient Global Impression of Change (PGI-C) scale at week 8. Secondary outcomes included changes in hair loss severity, 60 s hair count, depressive symptoms (PHQ-9), safety, and gut microbiome composition (Chinese Clinical Trial Registry ChiCTR2500112698). Results: At week 8, 62.5% (20/32) of participants reported PGI-C improvement. Significant reductions were observed in hair loss severity (p = 0.0008), 60 s hair count (p = 0.0048), and PHQ-9 scores (p = 0.002). Younger age was associated with PGI-C response (OR per year 0.86, 95% CI: 0.73-0.98, p = 0.037). Metagenomic analysis identified engraftment of B. longum HK003-like profiles in a subset of participants at week 12. Changes in microbial pathways related to thiamine metabolism, vitamin B12 salvage, and lipopolysaccharide biosynthesis were associated with ΔPHQ-9 (FDR-adjusted p < 0.05), but not with hair-related endpoints. No serious adverse events occurred. Conclusions: This first-in-human pilot study suggests that HQP08 was well tolerated and was associated with within-participant changes in hair-loss measurements and PHQ-9 scores. Randomized controlled trials are warranted to confirm efficacy and further elucidate mechanisms within the gut-brain-skin axis.},
}

Humans
Pilot Projects
*Alopecia/microbiology/therapy
Female
Male
Adult
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Synbiotics/administration & dosage
Treatment Outcome
*Depression/therapy/microbiology
*Bifidobacterium longum
Dietary Supplements
Young Adult

@article {pmid42884650,
year = {2026},
author = {Zhao, X and Yang, C and Gao, L and Gao, Y and Qian, W and Liu, H and Sun, Z and Wang, G and Zhao, F},
title = {Heat-Inactivated Lacticaseibacillus paracasei PC-01 Alleviates DSS-Induced Colitis in Mice by Modulating Gut Microbiota and Intestinal Barrier Function.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193199},
pmid = {42884650},
issn = {2072-6643},
support = {23402050//National Natural Science Foundation of China/ ; 2024YFA1307002//National Key Research and Development Program of China/ ; 2024QN03052//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; SPKJ202206//Science and technology project of the Food Science and Engineering College, Inner Mongolia Agricultural University/ ; },
mesh = {Animals ; Mice, Inbred C57BL ; *Lacticaseibacillus paracasei/physiology ; *Gastrointestinal Microbiome ; Mice ; Intestinal Barrier Function ; Dextran Sulfate ; *Colitis/chemically induced/microbiology/therapy ; Cytokines/blood/metabolism ; Disease Models, Animal ; Male ; Hot Temperature ; *Probiotics/pharmacology ; Intestinal Mucosa/microbiology/metabolism ; },
abstract = {Background: Inflammatory bowel disease (IBD) is a chronic, progressive, immune-mediated inflammatory disorder of the gastrointestinal tract. Methods: This study used C57BL/6J mice induced by DSS to construct an intestinal inflammation model, and explored the alleviating effect and potential mechanism of heat inactivated Lactobacillus paracasei PC-01 (PC-01) on intestinal inflammation. Results: The results showed that heat-inactivated PC-01 significantly decreased the Disease Activity Index and H&E histopathological scores (p < 0.05). It also reduced the serum levels of pro-inflammatory cytokines, including IL-6, IL-1β, TNF-α, and malondialdehyde (p < 0.01), increased the levels of the anti-inflammatory factor IL-10 (p < 0.001) and antioxidant enzymes SOD and GSH-Px (p < 0.01), and restored the integrity of the intestinal epithelial barrier in DSS-induced colitis mice. Metagenomic analysis showed that PC-01 treatment restored the abundance of beneficial bacteria, including Barnesiella and Muribaculum, and reduced the enrichment of opportunistic pathogens such as Angelakisella and Lawsonibacter (p < 0.05). Further functional annotation of the microbial community indicated that PC-01 significantly enriched pathways related to the TCA cycle, riboflavin metabolism, Toll and Imd signaling, and lipopolysaccharide biosynthesis. In addition, the relative abundances of auxiliary activities, polysaccharide lyases, and S-layer homology modules were lower than those in the DSS group, whereas those of glycoside hydrolases, glycosyltransferases, and carbohydrate esterases were higher. At the transcriptional level, intervention with heat-inactivated PC-01 resulted in a downward trend in the expression of TLR4, Nfkb1, and Rela, accompanied by reduced expression of the chemokines MCP-1 and Cxcl10, and inflammasome-related genes NLRP3, Casp1, and IL-1β. Conclusions: In summary, heat-inactivated Lacticaseibacillus paracasei PC-01 effectively alleviated intestinal inflammatory injury in mice by regulating gut microbiota homeostasis and suppressing intestinal inflammatory responses.},
}

Animals
Mice, Inbred C57BL
*Lacticaseibacillus paracasei/physiology
*Gastrointestinal Microbiome
Mice
Intestinal Barrier Function
Dextran Sulfate
*Colitis/chemically induced/microbiology/therapy
Cytokines/blood/metabolism
Disease Models, Animal
Male
Hot Temperature
*Probiotics/pharmacology
Intestinal Mucosa/microbiology/metabolism

@article {pmid42884898,
year = {2026},
author = {Li, J and Wang, Q and Li, X and Zhang, Z and Liu, Y and Meng, Q and Zou, J and Liu, X and Luo, Y and Guo, Z},
title = {Long-Term Fertilisation Regimes, Crop Yield and Rhizosphere Microecology in a Wheat-Soybean Rotation System.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193034},
pmid = {42884898},
issn = {2223-7747},
support = {2023YFD1500700//National Key Research and Development Program of China/ ; },
abstract = {Long-term fertilisation must sustain crop yield and rhizosphere microbial functions in wheat-soybean rotations, but interannual responses remain unclear. We examined 12 treatments in a long-term field experiment established in 1979 and continuing through 2025 in Heilongjiang, China; three within-plot soil composites per treatment represented the 2025 microbiome snapshot. Long-term wheat and soybean grain and straw yield, rhizosphere and non-rhizosphere metagenomes, bacterial diversity, functional gene profiles, taxonomic composition, yield-microbe correlations, and structural equation modelling were assessed. The displayed wheat grain yields differed among treatments, with the median approaching 2500 kg ha[-1] under manure plus medium-rate mineral fertiliser. Soybean grain yield exceeded 2000 kg ha[-1] under manure plus low- or medium-rate mineral fertiliser and was higher than under high-rate mineral fertiliser alone. Separate exploratory treatment-only PERMANOVAs returned R[2] values of 0.7578 and 0.8227 for rhizosphere and non-rhizosphere functional profiles, respectively; the profiles were within-plot subsamples. Mesorhizobium, Lysobacter, Gemmatirosa, and Pseudolabrys were positively correlated with crop yield. Structural equation modelling linked available phosphorus to wheat yield and rhizosphere diversity and linked available potassium to soybean yield. These descriptive findings suggest crop-specific fertilisation patterns and possible associations of yield with soil nutrients and rhizosphere microbiota, indicating that productivity and microbial responses should inform long-term nutrient management.},
}

@article {pmid42885240,
year = {2026},
author = {Ghosh, SK and Wassel, MA and Wong, MK and Hyodo, S and Hamasaki, K},
title = {Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70448},
doi = {10.1111/1462-2920.70448},
pmid = {42885240},
issn = {1462-2920},
support = {//University of Tokyo/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; *Oncorhynchus keta/microbiology/metabolism/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Amino Acids/biosynthesis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; },
abstract = {The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.},
}

Animals
*Oncorhynchus keta/microbiology/metabolism/genetics
Metagenomics
*Gastrointestinal Microbiome
Amino Acids/biosynthesis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome

@article {pmid42885446,
year = {2026},
author = {Deng, Q and Lv, L and Feng, H and Liu, D and Wang, F and Wang, J and Liu, X and Sun, S and Huang, B},
title = {Effects of a bioherbicide and a chemical herbicide on soil microbial community structure, diversity, and nitrogen cycling functions.},
journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/03601234.2026.2745422},
pmid = {42885446},
issn = {1532-4109},
abstract = {The fermentation broth of the bioherbicidal fungus Aspergillus versicolor D5 shows efficacy against dicotyledonous weeds in tobacco fields. However, little is known about its impact on the soil ecological environment of tobacco fields, particularly in comparison with chemical herbicides. This study compares the effects of a bioherbicide (BIO) and rimsulfuron (CHE) on tobacco field soil ecology. Both show comparable weed control efficacy and increase urease and dehydrogenase activities, although BIO causes a smaller urease increase. Unlike CHE, BIO does not inhibit nitrite reductase. Metagenomics shows that BIO slightly alters community structure without reducing diversity, whereas CHE decreases it. BIO increases the abundance of Luteitalea (involved in decomposing complex organic carbon and nitrogen cycling) and Chloracidobacterium (light-assisted carbon metabolism) within the phylum Acidobacteria, whereas CHE significantly reduces the abundance of these bacteria. BIO decreases the abundance of arbuscular mycorrhizal fungi Rhizophagus and Funneliformis, while CHE increases them. Nitrogen cycling analysis shows that BIO only significantly reduces the anammox pathway, causing little overall disturbance, whereas CHE strongly promotes dissimilatory/assimilatory nitrate reduction and nitrate/nitrite uptake pathways. These findings indicate that the fermentation extract of A. versicolor D5 affects soil ecology less than rimsulfuron, causing less disturbance to soil microbial diversity in this study.},
}

@article {pmid42885648,
year = {2026},
author = {Pinson, M and Croville, G and Crispo, M and Gaide, N and Walch, M and Viloux, N and Bourgeois, C and Sraka, B and Belloc, C and Guerin, JL},
title = {Emerging enteric coronaviruses in captive-bred red-legged partridges (Alectoris rufa), France.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/03079457.2026.2723911},
pmid = {42885648},
issn = {1465-3338},
abstract = {Enteritis syndrome in French red-legged partridge flocks.Detection of novel enteric coronaviruses (ParCoVs).ParCoVs are phylogenetically close to French TCoVs.Significant genetic variability of ParCoVs ruled out a clonal cluster of cases.Avian coronavirus RNA detected in intestinal sections by RNAscope ISH.},
}

@article {pmid42885911,
year = {2026},
author = {Xu, C and Wu, X and He, Q and Yang, L and Talib, S and Li, K},
title = {The Qing Chang Hua Shi Formula combined with allicin alleviates Cryptosporidium parvum infection in immunosuppressed mice and is associated with restoration of NLRP6, IL-18, IFN-γ, and intestinal microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0366225},
doi = {10.1128/spectrum.03662-25},
pmid = {42885911},
issn = {2165-0497},
abstract = {Cryptosporidium parvum is a highly pathogenic zoonotic parasite with limited therapies. Current study explored the anti-C. parvum effect of Qing Chang Hua Shi Formula (QHF) and allicin in vitro in immunosuppressed mice. In vitro, QHF and allicin inhibited over 90% of C. parvum. In vivo, the 8-day treatment reduced fecal oocyst shedding to 12.88% of the model group. Infection disrupted intestinal homeostasis, reduced tight-junction protein expression, and downregulated NLRP6, while inducing systemic inflammation and elevating IL-18/IFN-γ levels, which were further increased by treatment. Treated mice also showed increased abundance of Archangium and Corallococcus and decreased abundance of Clostridioides and Butyricimonas. Predicted microbial functional pathways revealed enrichment of glycolysis-related genes (L-lactate dehydrogenase [LDH], glyceraldehyde-3-phosphate dehydrogenase [GAPDH]) in infected mice, with treatment-associated shifts in amino acid synthesis pathways. Molecular docking suggested potential binding of benzoylpaeoniflorin, baicalin, and wogonoside to C. parvum LDH, ATP/ADP translocase, and gp40/15. Together, these findings indicate that QHF combined with allicin alleviates C. parvum infection in immunosuppressed mice and is associated with restoration of intestinal barrier markers, immune responses, and gut microbiota composition, suggesting a potential therapeutic approach for cryptosporidiosis.IMPORTANCECurrent study demonstrates that Qing Chang Hua Shi Formula (QHF) combined with allicin effectively inhibits Cryptosporidium parvum proliferation and concurrently mitigates intestinal damage and dysbiosis induced by C. parvum infection. QHF treatment was associated with upregulation of NLRP6, improved gut microbiota profiles, and elevated IFN-γ levels. These changes correlated with reduced parasite burden and alleviated intestinal injury, suggesting a potential immunomodulatory role that warrants further mechanistic investigation. Metagenomics disclosed that QHF and allicin were associated with changes in predicted microbial functional pathways, including those involved in glycolysis and amino acid metabolism, and with enrichment of certain bacterial taxa, such as Corallococcus and Archangium. Molecular dynamics simulations suggested that benzoylpaeoniflorin and baicalin may bind stably to C. parvum L-lactate dehydrogenase (LDH) and ATP/ADP translocase, raising the hypothesis that they could interfere with parasite energy metabolism. However, enzymatic validation is required to confirm this possibility. These findings suggest a potential therapeutic approach for cryptosporidiosis and highlight alterations associated with C. parvum infection.},
}

@article {pmid42885945,
year = {2026},
author = {Shremo Msdi, A and Begum, K and Hu, C and Shaw, N and Mai, A and Alam, MJ and Bassères, E and Eubank, T and Yu, XY and Mortin, LI and Silverman, MH and Garey, KW},
title = {The effects of novel oral preclinical PolC inhibitor antibiotic candidates on the gut microbiome in a murine thigh infection model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0114326},
doi = {10.1128/spectrum.01143-26},
pmid = {42885945},
issn = {2165-0497},
abstract = {UNLABELLED: Antibiotics can negatively affect gut microbiome composition and function. However, preclinical evaluations of antibiotic effects on the microbiome are rarely undertaken. The purpose of this study was to characterize pharmacokinetics and metagenomic profiles of PolC inhibitor compounds compared to linezolid in a neutropenic murine thigh infection model. Neutropenic mice thighs were inoculated with methicillin-resistant Staphylococcus aureus (MRSA) and dosed orally starting 1 h later with ACX-728, ACX-801, ACX-978, or linezolid. Untreated control mice were euthanized at 1 h for baseline data, and a second untreated group were euthanized at 24 h after the start of dosing, when all remaining mice were euthanized. At euthanasia, thigh muscles were excised for MRSA quantification, and fecal pellets, colon tissue, and plasma samples were collected for drug concentration and microbiome analyses. All PolC inhibitors were detectable in plasma and feces at 25 h. Compared with linezolid, PolC inhibitors maintained greater gut microbial richness and diversity in this acute murine infection model. PolC-treated samples preserved overall community structure and Bacteroidota dominance, whereas linezolid induced marked disruption, with secondary expansion of Pseudomonadota, primarily Escherichia coli. Microbial pathway analysis showed preservation of community-level metabolic function for PolC inhibitors but marked disruption by linezolid. Compared to controls, linezolid produced a 4.4 log reduction in MRSA colony-forming unit per gram, while the PolC inhibitors produced a mean log reduction of 0.4-2.5 per group. In these exploratory studies, PolC inhibitor compounds preserved anaerobic community structure and fermentative capacity, whereas linezolid induced depletion of healthy commensals and expansion of aerotolerant taxa. These findings highlight the importance of microbiome-informed antibiotic evaluation in preclinical studies. Larger preclinical and clinical studies are warranted to confirm these findings.

IMPORTANCE: This study evaluated the class effect of PolC inhibitors on the microbiome as part of the preclinical development plan for systemic PolC inhibitors. Similar to the non-absorbable antibiotic, ibezapolstat, a narrow effect on the microbiome was observed with these novel compounds.},
}

@article {pmid42874258,
year = {2026},
author = {Zhang, J and Li, J and Qi, J and Zhang, L and Wang, Y and Cheng, D and Zhou, G and Yang, G and Liu, H},
title = {Operational reliability of full-scale activated sludge systems under carbon-source substitution with fermentation-derived yellow water: organic risk attenuation and microbial community stability.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131175},
doi = {10.1016/j.jenvman.2026.131175},
pmid = {42874258},
issn = {1095-8630},
abstract = {Fermentation-derived waste streams have attracted increasing attention as sustainable alternative carbon sources for biological nitrogen removal in municipal wastewater treatment plants (WWTPs). However, their operational reliability remains insufficiently understood because previous evaluations have focused primarily on conventional treatment performance while overlooking the fate of complex organic constituents and microbial responses to chemically heterogeneous carbon inputs. In this study, a full-scale municipal WWTP was investigated to evaluate carbon-source substitution with fermentation-derived yellow water. Carbon-source substitution maintained stable COD, NH4[+]-N, TN, and TP removal throughout operation, with effluent quality consistently meeting the Chinese Class IA discharge standard. Fifteen representative organic constituents with different predicted hazard potentials were identified in yellow water, all of which exhibited substantial attenuation (approximately 50-99%) during biological treatment, including compounds with relatively higher predicted toxicity. Microbial community composition remained relatively stable during carbon-source substitution, while genes associated with nitrogen cycling, aromatic compound degradation, and oxidative stress response remained consistently represented. Genome-resolved metagenomic analysis further demonstrated that representative microbial populations encoded genes spanning these three functional categories. These findings demonstrate the feasibility of using fermentation-derived yellow water as an alternative external carbon source in full-scale WWTPs and extend current evaluation of waste-derived carbon sources beyond conventional treatment performance by incorporating organic risk attenuation and microbial functional adaptation.},
}

@article {pmid42874260,
year = {2026},
author = {Ghaly, TM and McPherson, VJ and Rajabal, V and Ghaly, ME and Taws, N and Gallagher, RV and Le Roux, JJ and Tetu, SG},
title = {Soil microbial traits shift on contrasting timescales following restoration of former grazing lands.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131161},
doi = {10.1016/j.jenvman.2026.131161},
pmid = {42874260},
issn = {1095-8630},
abstract = {Native vegetation restoration is a key strategy for restoring degraded lands globally. While this process can reshape belowground microbial communities, the extent to which such changes restore soil ecosystem functions, and whether different microbial traits recover synchronously or on distinct timescales remains less clear. Understanding the sequence of functional recovery is essential for evaluating restoration success, as distinct microbial traits drive different ecosystem services, from carbon storage to plant growth promotion, and serve as meaningful indicators of long-term ecological recovery. To address this, we applied deep metagenomic sequencing to characterise soil microbial responses following native vegetation restoration (spanning 1-31 years prior to sampling) on grazing agricultural lands. We found that microbial functional changes occurred in distinct phases: an early, rapid restructuring of core soil health processes, detectable as early as three years, including enrichment of nutrient retention and carbon fixation pathways, followed by a more gradual development of plant growth-promoting traits as the plant community matures. Genome-resolved analyses of nearly 500 metagenome-assembled genomes revealed a fundamental shift in dominant microbial life history strategies. Specifically, communities transitioned from a resource-scavenging and stress tolerance profile in grazing soils to strategies that prioritise biosynthesis and growth yields in restored soils. These lifestyle shifts have important implications for enhancing the microbial biomass and carbon sink potential of soils. Together, these findings show that microbial functional shifts following restoration are temporally structured - informing expectations for when key restoration targets may be achieved, and providing a practical framework for monitoring ecosystem recovery.},
}

@article {pmid42874465,
year = {2026},
author = {Orf, GS and Berg, MG and Pantsulaia, M and Vardiashvili, M and Galdavadze, K and Biswas, RSR and Bishop, J and Sequeira, AF and Khoperia, A and Alkhazashvili, M and Cloherty, GA},
title = {Disparate tetraparvovirus species linked to hepatitis.},
journal = {Virology},
volume = {625},
number = {},
pages = {111096},
doi = {10.1016/j.virol.2026.111096},
pmid = {42874465},
issn = {1096-0341},
abstract = {The role of human tetraparvoviruses (PARV4) in cases of acute illness is poorly characterized, and the contribution of animal-associated tetraparvoviruses to human disease is unknown. In this study, we applied metagenomic and viral-enrichment next-generation sequencing to plasma from patients with diagnostically unresolved acute illness in Georgia (non-A-C hepatitis) and Bangladesh (acute febrile illness), and two tetraparvovirus genomes were recovered. Specimen HEP004 from a Georgian patient with acute hepatitis contained a virus clustering within Tetraparvovirus ungulate4, a species associated with sheep and goats, representing the first detection of this species in human plasma. Specimen 39HEP0432 from a Bangladeshi patient with fever and jaundice contained a human PARV4 grouping within a clade of genotype 2 previously reported in pediatric acute encephalitis cases in South Asia. Within-host minor variation was detected in both genomes, raising the possibility of ongoing replication. Phylogenetic and ancestral sequence analyses of human PARV4 genotype 2 identified lineage-defining capsid amino acid substitutions in the South Asian clade (which 39HEP0432 shared), situated in surface-exposed positions that may influence viral tropism or host immune interactions. These findings expand the known diversity of tetraparvoviruses detected in humans, including an ungulate-associated species with possible zoonotic potential, and provide sequence data to support targeted screening in cases of unexplained hepatitis and febrile illness.},
}

@article {pmid42874540,
year = {2026},
author = {Dara, M and Calabrisotto, LS and Bisanti, L and Torreagrossa, N and La Corte, C and Bertini, F and Catania, V and Quatrini, P and Parrinello, D and Piazzese, D and Cammarata, M and Banni, M and Parisi, MG},
title = {Integrated assessment of bioplastic materials effects on microbial communities and macroinvertebrate model, Mytilus galloprovincialis, in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120459},
doi = {10.1016/j.marpolbul.2026.120459},
pmid = {42874540},
issn = {1879-3363},
abstract = {The increasing use of biopolymer derivatives raises concerns about their actual environmental sustainability, which remains insufficiently understood. In this study, we adopted an integrated approach combining microbial and ecotoxicological perspectives to evaluate their impact in marine ecosystems. We investigated the plastisphere composition of conventional petroleum-based High Density Polyethylene (HDPE) and polyhydroxyalkanoates (PHA), polyhydroxybutyric acid (PHB), and polylactic acid (PLLA) scaffolds after 60 days of exposition in marine ecosystem or microcosm, by high throughput metagenomics 16S rRNA gene sequencing and culture dependent approach. A variation in terms of composition and abundance of plastisphere, between petroleum-derived and bio-based degradable scaffolds, was observed. A high abundance of Proteobacteria was detected in all polymers, with Alpha and Gamma Proteobacteria dominant. At the genera level, high abundance of sequences assigned to hydrocarbon-degrading bacteria (i.e. Oleibacter, Labrenzia, Alcanivorax) was detected in biopolymeric plastic compared to petroleum-based plastic. To link microbial colonization and material degradation with biological effects on marine fauna, the impact of biopolymer-derived micro- and nanoparticles on the mussel Mytilus galloprovincialis was assessed. Both in vitro and in vivo assays demonstrated immune system activation through phagocytosis and encapsulation, while in vivo exposures influenced several biomarkers (phagocytosis, haemocyte density, lysozyme, glutathione peroxidase, phenoloxidase, alkaline phosphatase, esterase), suggesting potential detrimental effects after 72 h. By bridging microbial ecology with immunological responses in a bioindicator species, this multidisciplinary study provides novel insights into the complex ecological footprint of biodegradable plastics in marine environments.},
}

@article {pmid42874563,
year = {2026},
author = {Ako, BAA and Assohoun, SE and Diplo, BFT and Coulibaly, TGS and Acquah, JQ and Touré, AO and Kadjo, HAA and Gbonon, CV and Djaman, JA and Dosso, M},
title = {Establishing a genomic lab during COVID-19: A perspective from Institut Pasteur in Côte d'Ivoire.},
journal = {Cell genomics},
volume = {6},
number = {10},
pages = {101385},
doi = {10.1016/j.xgen.2026.101385},
pmid = {42874563},
issn = {2666-979X},
mesh = {Cote d'Ivoire/epidemiology ; Humans ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics ; *Genomics ; *Laboratories/organization & administration ; Pandemics ; *Academies and Institutes/organization & administration ; },
abstract = {Africa bears a disproportionate burden of epidemic threats, exemplified by COVID-19. Drawing on lessons from the pandemic, we describe how Institut Pasteur de Côte d'Ivoire transitioned from limited capacity to established expertise in genomic surveillance. This institutional strengthening provides a strategic blueprint for enhancing Africa's resilience against emerging health threats.},
}

Cote d'Ivoire/epidemiology
Humans
*COVID-19/epidemiology/virology
*SARS-CoV-2/genetics
*Genomics
*Laboratories/organization & administration
Pandemics
*Academies and Institutes/organization & administration

@article {pmid42874851,
year = {2026},
author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sangtian, M and Viangteeravat, T and Sriswasdi, S},
title = {Potential clinical actionability of metagenomic next-generation sequencing for antimicrobial stewardship for urinary tract infections: a retrospective, single-centre, BI-Biotia UTI cohort study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109181},
doi = {10.1016/j.ijid.2026.109181},
pmid = {42874851},
issn = {1878-3511},
abstract = {OBJECTIVES: Culture and antimicrobial susceptibility testing (AST) take 48-72 hours, leaving empirical therapy for urinary tract infections (UTIs) without resistance data. Metagenomic next-generation sequencing (mNGS) reports resistance within hours, but its potential clinical actionability for prescribing is underexplored.

METHODS: In a retrospective single-centre cohort (Bangkok tertiary hospital, 2018-2020), BIOTIA-DX results were compared with culture and AST in 251 culture-paired samples. Potential clinical actionability was assessed for 54 same-day empirical prescriptions and a post hoc ablation estimated what a rule-based policy would have prescribed under different information from mNGS.

RESULTS: Twenty-two of 54 prescriptions (40·7%, 95% CI 28·7-54·0) were potentially actionable: treatment failure prevention 9 (16·7%) and de-escalation 13 (24·1%). Excluding blaEC and blaACT raised cephalosporin specificity from 25·6% to 78·9% with a small tradeoff in sensitivity. NPVs were at least 89·7% for carbapenems, cephalosporins, trimethoprim/sulfamethoxazole, aminoglycosides and the fluoroquinolone classifier reached 100·0% PPV in Escherichia coli. Our refined resistance classification rules achieved a good tradeoff between the risk of ineffective antibiotics and the use of broad-spectrum carbapenem, compared with observed prescribing.

CONCLUSIONS: In a high-resistance setting, a same-day mNGS report was potentially actionable for two in five empirical prescriptions, mainly through resistance calling. However, the findings rest on a small number of cases.},
}

@article {pmid42874903,
year = {2026},
author = {Zhang, Y and Liu, H and Wang, P and Liu, H and Jing, H},
title = {Ecological partitioning and functional specialization of Thermoproteota across multiple trench sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125897},
doi = {10.1016/j.envres.2026.125897},
pmid = {42874903},
issn = {1096-0953},
abstract = {Thermoproteota (formerly referred to as Thaumarchaeota) are phylogenetically divided into ammonia-oxidizing archaea (AOA) affiliated with Nitrososphaeria and basal non-ammonia-oxidizing archaea (non-AOA). While both groups co-existed in the hadal trenches, their differentiations across multiple trenches remain poorly understood. Here, 25 medium- and high-quality metagenome-assembled genomes (MAGs), including 18 AOA and 7 non-AOA representatives, were generated from metagenomics of Diamantina, Kermadec, Mariana-Yap trench sediments. AOA MAGs of Nitrosopumilales encompassing CSP1-1, DRGT01 and Nitrosopumilus exhibited chemoautotrophic potential with broader niche widths and higher diversity across trenches. Potential nitrification rates (PNR) were predominantly associated with AOA activity and exhibited clear depth-/trench-dependent patterns, driven by NH4[+] availability. In contrast, the non-AOA lineage diverged approximately earlier (∼2.66 Ga), whereas the divergence between B1T1B5 and JAPUIC01 was estimated at ∼1.91 Ga during the Paleoproterozoic. B1T1B5 harbored auto/mixotrophic traits, whereas JAPUIC01 exhibited a metabolically flexible, heterotrophic strategy potentially suited to anaerobic niches. The pronounced niche partitioning and functional specialization of AOA and non-AOA Thermoproteota across geographically isolated trenches were based on their genomic traits, likely an integrated consequence of microbial ecological adaptation and strong purifying selection of the local environmental condition. The findings provide a unified ecological and evolutionary framework for understanding Thermoproteota diversification in the deep ocean and reveals how functional specialization and genomic adaptive evolution shape nitrogen cycling in Earth's deepest ecosystems.},
}

@article {pmid42875116,
year = {2026},
author = {Díaz Escandón, D and Acton, A and Coppins, BJ and Thai, T and Spribille, T},
title = {The lichen symbiont Wadeana represents an independent origin of hysterothecial fungi in the Eurotiomycetes.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101841},
doi = {10.1016/j.funbio.2026.101841},
pmid = {42875116},
issn = {1878-6146},
mesh = {*Symbiosis ; Phylogeny ; *Lichens/microbiology/physiology ; *Ascomycota/classification/genetics/physiology/isolation & purification ; Sequence Analysis, DNA ; DNA, Fungal/genetics/chemistry ; Genome, Fungal ; },
abstract = {The genus Wadeana was erected almost fifty years ago to accommodate an unusual pair of lichen fungal symbionts with hysterothecial ascomata and polysporous asci associated with the algal genus Trentepohlia. The evolutionary position of Wadeana has long been unclear, and the genus has variably been treated as a dothideomycete, as incertae sedis or, recently, within the subclass Acarosporomycetidae of the Lecanoromycetes. Here we present multilocus evidence from metagenome-assembled genomes from the generitype, Wadeana dendrographa, that place it with strong support as sister to all genera currently treated in the order Sclerococcales in the subclass Sclerococcomycetidae of the Eurotiomycetes. Wadeana represents the first confirmed case of hysterothecial ascomata in Eurotiomycetes. We compare evidence for its status as a lichen symbiosis with examples of fungal-algal interactions in other members of the Sclerococcomycetidae. Finally, we also describe a new family (Wadeanaceae) and order (Wadeanales) to accommodate Wadeana and a new subclass (Xylobotryomycetidae) to accommodate the order Xylobotryales in the Eurotiomycetes.},
}

*Symbiosis
Phylogeny
*Lichens/microbiology/physiology
*Ascomycota/classification/genetics/physiology/isolation & purification
Sequence Analysis, DNA
DNA, Fungal/genetics/chemistry
Genome, Fungal

@article {pmid42875131,
year = {2026},
author = {Kang, C and Zheng, X and Liu, Z and Wang, W and Zeng, W and He, Y and Huang, J and Nie, W and Wang, J and Wang, F},
title = {Cryptic microheterogeneity of the casing-layer microbiome and metabolome is associated with primordium fate in Phallus rubrovolvatus.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101864},
doi = {10.1016/j.funbio.2026.101864},
pmid = {42875131},
issn = {1878-6146},
mesh = {*Microbiota ; *Metabolome ; *Agaricales/growth & development/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {Commercial cultivation of Phallus rubrovolvatus relies on casing layers, yet yields remain unstable, with primordium development varying among individual microsites. This cryptic microheterogeneity is masked by conventional bulk sampling, limiting insight into casing-layer performance. Here, we combined phenotype-guided back-tracing with multi-omics to characterize microecological signatures associated with primordium fate. We identified two contrasting ecological regimes associated with reproductive outcomes. Productive microsites were characterized by a "Cooperative state" enriched in oligotrophic bacteria (e.g., Hyphomicrobium) and basidiomycetes (e.g., Clathrus columnatus). Productive microsites also showed lower available potassium (K[+]) and elevated catalase activity. Conversely, non-productive microsites were characterized by a Rhizopus-dominated "Disruptive state". This state was associated with elevated urease activity, lower catalase activity, and stress-associated metagenomic functional signatures. Overall, primordium fate was associated with distinct local microbial, functional, and metabolic configurations that were not fully explained by bulk physicochemical properties. We propose the "Cooperative vs. Disruptive" model as a conceptual framework and identify candidate microbial and metabolic features for future validation in microbiome-informed cultivation management.},
}

*Microbiota
*Metabolome
*Agaricales/growth & development/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Multiomics

@article {pmid42875451,
year = {2026},
author = {Aguilar, A and Miranda Perez, I and Nadel, O and Nayfach, S and Ruiz Pestana, L and Segall, AM and Rohwer, FL and Roux, S and White, S and Luque, A},
title = {Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42875451},
issn = {2041-1723},
support = {GBMF9871//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2424579//National Science Foundation (NSF)/ ; },
mesh = {*Capsid/metabolism/chemistry ; *Evolution, Molecular ; Genome, Viral ; Phylogeny ; Models, Molecular ; *DNA Viruses/genetics ; *Capsid Proteins/genetics/chemistry/metabolism ; Protein Folding ; },
abstract = {The HK97-fold is an ancient, conserved protein structure that assembles protein shells, forming the capsids of Duplodnaviria viruses and prokaryotic biochemical compartments called encapsulsins. It has been proposed that encapsulins evolved from HK97-fold viruses. But the higher complexity of viral capsids represents a biophysical paradox in the evolution of HK97-fold protein shells. To resolve this problem, we hypothesize the existence of simpler HK97-fold viral capsids associated with smaller genomes than those of known HK97-fold viruses. Such small viral genomes are searched in environmental metagenomes across public databases, including IMG/M and MGnify. Using hidden Markov models and protein language models, we identify and characterize small viral genomes encoding HK97-fold proteins that exhibit molecular similarities to encapsulins yet lack portal and tail genes. The phylogenetic analyses of HK97-fold proteins reveal independent mixed groups of viruses and encapsulins, and structural analyses identify similarities between encapsulins and procapsids, the immature state of viral capsids. The observations support a bidirectional evolution between encapsulins and HK97-fold viruses enabled by the viral procapsid state. Using biophysical and genomic arguments, we introduce an evolutionary model of HK97-fold protein shells, predicting that they emerged as lower-symmetry biochemical compartments and that HK97-fold viral capsids may retain biochemical functions.},
}

*Capsid/metabolism/chemistry
*Evolution, Molecular
Genome, Viral
Phylogeny
Models, Molecular
*DNA Viruses/genetics
*Capsid Proteins/genetics/chemistry/metabolism
Protein Folding

@article {pmid42876496,
year = {2026},
author = {Yue, C and Xia, B},
title = {Case Report: Necrotizing fasciitis caused by Vibrio vulnificus without recalled seafood or seawater exposure diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1963954},
pmid = {42876496},
issn = {2296-858X},
abstract = {Vibrio vulnificus is a highly virulent marine Gram-negative pathogen that rapidly induces soft tissue necrosis and fatal septic shock, with infections generally linked to raw seafood ingestion or open wound contact with seawater. We report an atypical severe case of V. vulnificus septic shock in a 60-year-old male patient without recalled seafood or seawater exposure and without classic underlying high-risk diseases such as liver cirrhosis and diabetes mellitus. The patient presented with rapidly progressive swelling and subcutaneous ecchymosis of the right lower limb, which quickly deteriorated into refractory septic shock within 24 h. Conventional empiric broad-spectrum antibiotics failed to halt disease progression before pathogen identification. Metagenomic next-generation sequencing (mNGS) rapidly detected V. vulnificus sequences on the second admission day, and the diagnosis was further confirmed by blood culture. Multidisciplinary interventions including repeated radical surgical debridement, vacuum sealing drainage (VSD), targeted anti-infective therapy and comprehensive organ support finally achieved complete recovery. The patient recovered normal walking function during six-month outpatient follow-up. This rare occult infection case reminds clinicians to maintain high suspicion of V. vulnificus infection for rapidly advancing necrotizing fasciitis combined with septic shock, even when no aquatic exposure is recalled. Meanwhile, this work validates the critical value of mNGS for early pathogen identification in unexplained life-threatening sepsis.},
}

@article {pmid42876542,
year = {2026},
author = {Starikova, EV and Kuzmichenko, PA and Fedorov, DE and Vvedensky, AV and Pavlenko, AV and Arkhipova, AL and Kovalchuk, SN and Ilina, EN},
title = {Gut microbiome resistotypes reflect chronological age and Enterobacteriaceae relative abundance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869983},
pmid = {42876542},
issn = {1664-302X},
abstract = {BACKGROUND: Surveillance of antibiotic resistance genes (ARGs) in the human gut microbiota is critical for informing public health interventions and antibiotic stewardship strategies, taking into account sociodemographic, behavioral, and health-related factors. Although metagenomics research has grown exponentially, few studies have described resistome dynamics over time. In this study, we investigated resistome profiles over a 5-year interval (between 2016-2017 and 2022) in adult residents of Arkhangelsk, Northwestern Russia.

RESULTS: Over 5 years, we observed an increase in ARGs richness and abundance along with the prevalence changes in genes conferring resistance to aminoglycosides (aph2, aph3, ant9), lincosamides (lnuC), chloramphenicol (cat, catA), and macrolides (ermG, ermB). We have identified two resistotypes in our data that differed in the number of identified ARGs. The less frequent resistotype 2, characterized by a higher number of ARGs, was associated with higher participants' chronological age and increased Enterobacteriaceae abundance. Approximately one-third of the participants have shifted from one resistotype to another within a 5-year period. Temporal changes in resistome profiles occurred unevenly among participants, with the greatest changes noted for 41-45 and 61-65 age groups. No associations were found between COVID-19 history and resistome composition.

CONCLUSIONS: We showed an increase in overall ARG richness, ARG abundance, and the prevalence of certain ARGs in microbiomes of adult residents of Arkhangelsk over a 5-year period. We have identified two resistotypes; the one with higher ARGs richness was linked to higher chronological age and Enterobacteriaceae family relative abundance. These findings underscore the necessity for further antibiotic resistance surveillance to address the accelerating global dissemination of ARGs, while highlighting age as an underrecognized factor contributing to resistome dynamics.},
}

@article {pmid42876655,
year = {2026},
author = {Shi, X and Xu, H and Li, W and Wang, J and Song, Y and Yang, M and Wang, B and Liu, CQ},
title = {Evolution of lake microbial structure and function under climatic and anthropogenic forcings: Insights from sedimentary ancient DNA.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117760},
pmid = {42876655},
issn = {2589-0042},
abstract = {Structure and function of lake microorganisms are sensitive to environmental disturbances; yet their differential responses to climatic and anthropogenic forcings over centennial scales remain poorly understood. Here, we analyzed a sediment core from Lake Daihai in northern China, combining metagenomics and stable isotope analyses. Our results revealed that microbial community assembly was dominated by deterministic processes, whereas stochasticity increased notably after 1850, coinciding with the termination of the Little Ice Age and intensified human impacts. Notably, microbial community structure evolved at a rate approximately one order of magnitude faster than community function. This decoupling was mediated by functional redundancy associated with bacterial keystone taxa, ultimately resulting in more negative sedimentary carbon and nitrogen isotopic compositions nearly a century later. Gene-level functional redundancy further buffered ecosystem function variability across biological scales. Collectively, our findings integrate omics and geochemical approaches to advance the understanding of lake ecological evolution under complex multi-forcing regimes.},
}

@article {pmid42876743,
year = {2026},
author = {Tie, X and Sun, X},
title = {Pneumococcal meningitis secondary to chronic orbital inflammation with skull base erosion: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1918613},
pmid = {42876743},
issn = {2296-858X},
abstract = {This case report describes a 32-year-old female patient who developed acute pneumococcal meningitis following six-year chronic orbital inflammatory changes after strabismus corrective surgery. The patient experienced gradual deterioration of right-eye vision and recurrent retro-orbital headache; serial magnetic resonance imaging (MRI) from 2021 to 2023 demonstrated diffuse intraconal retrobulbar abnormalities and extraocular-muscle thickening. She subsequently presented with high fever, generalized seizures and impaired consciousness. Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Streptococcus pneumoniae and low-abundance Epstein-Barr virus (EBV) DNA; Active EBV-associated central nervous system infection could not be confirmed in the absence of CSF quantitative EBV polymerase chain reaction (PCR), EBV serology and immune-status testing. The patient received broad-spectrum intravenous antimicrobial, antiviral and glucocorticoid therapy, followed by endoscopic endonasal resection of inflammatory lesions at the ethmoid-skull-base complex. Histopathological examination of surgical specimens revealed non-specific inflammatory granulation tissue, and Langerhans cell histiocytosis was excluded. At six-month follow-up, the patient remained seizure-free; infectious foci showed near-complete resolution on imaging, yet mild residual orbital-leptomeningeal abnormalities persisted with modest visual improvement. This case demonstrates the potential for delayed intracranial extension from long-standing chronic orbital inflammation and highlights both the diagnostic utility and interpretive limitations of CSF-mNGS in clinical practice.},
}

@article {pmid42876779,
year = {2026},
author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Obi, AMM and Nguema, OAM},
title = {The mosquito gut microbiome and Plasmodium development: a scoping review of molecular approaches and implications for malaria vector control.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1906816},
pmid = {42876779},
issn = {2235-2988},
mesh = {Animals ; *Malaria/prevention & control/transmission/parasitology ; *Plasmodium/growth & development ; *Mosquito Vectors/microbiology/parasitology ; *Gastrointestinal Microbiome ; *Anopheles/microbiology/parasitology ; *Mosquito Control/methods ; Metagenomics ; Humans ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Malaria remains a major health burden, with an estimated 282 million cases and approximately 610,000 deaths recorded in 2024. The increasing prevalence of insecticide-resistant Anopheles vectors and drug-resistant Plasmodium strains has substantially eroded the efficacy of conventional control strategies, underscoring the critical need for innovative approaches. Accumulating evidence suggest that the mosquito midgut microbiome exerts a significant influence on Plasmodium sporogonic development; however, no scoping investigation has fully mapped the metagenomic evidence base in this field.

METHODS: Adhering to the Arksey and O'Malley framework and PRISMA-ScR guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science for publications from January 2000 to April 2026. Studies that used microbiological, molecular, or metagenomic techniques to study the gut microbiota of mosquito species related to Plasmodium were included. Descriptive mapping was used to synthesize the data in a thematic manner.

RESULTS: Thirteen primary studies met the inclusion criteria, comprising both observational field surveys and experimental infection studies. Four themes emerged: (1) gut microbiota diversity and composition are associated with Plasmodium infection status, though the direction varies by mosquito species, geography, and season; (2) several taxa, including Burkholderia, Asaia, Sphingomonas, Pseudomonas, and Serratia, are consistently associated with reduced infection or are experimentally inhibitory; (3) the Enterobacteriaceae and Serratia spp. show context-dependent, bidirectional relationships with Plasmodium that are best explained by strain-level variation; and (4) a smaller set of taxa, including Elizabethkingia, Chryseobacterium, Methylobacterium, and Pantoea, is positively associated with infection, on observational evidence only. The evidence relied predominantly on 16S rRNA amplicon sequencing, with a minority of studies adding whole-genome sequencing, transcriptomics, or metabolomics; none used shotgun metagenomics.

CONCLUSIONS: The mosquito gut microbiome exerts a net inhibitory effect on Plasmodium development, with translational potential for microbiome-based vector control, including paratransgenesis. However, the microbiota is not uniformly antagonistic to the parasite, and taxa positively associated with infection remain observational. The field is limited by a near-exclusive reliance on 16S rRNA profiling, few functional and longitudinal studies, and geographically narrow evidence. Multi-omics approaches, longitudinal designs, and broader geographic coverage will be essential to translate these associations into sustainable malaria control.},
}

Animals
*Malaria/prevention & control/transmission/parasitology
*Plasmodium/growth & development
*Mosquito Vectors/microbiology/parasitology
*Gastrointestinal Microbiome
*Anopheles/microbiology/parasitology
*Mosquito Control/methods
Metagenomics
Humans
Bacteria/classification/genetics

@article {pmid42876851,
year = {2026},
author = {Xie, W and Lu, S and Liu, Z and Zheng, J and Mo, F and Zhang, K and Huang, Z},
title = {Gut microbiome profiles of two limestone forest-dwelling langurs show stronger influence of host-associated factors than environment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953526},
pmid = {42876851},
issn = {1664-302X},
abstract = {BACKGROUND: Host-associated factor and the environment play crucial roles in shaping the composition and function of the gut microbiome. Considerable debate exists regarding the relative influence of host-associated and environmental factors on the gut microbiome. To determine the relative importance of host-associated factors and environmental factors in langurs, we employed metagenomic sequencing to examine differences in the gut microbiome of the white-headed langurs (Trachypithecus leucocephalus) and François' langurs (T. francoisi).

RESULTS: The results revealed that the alpha diversity of the gut microbiome significantly differed between white-headed langurs and François' langurs in similar habitats. However, there was no significant variation in the alpha diversity between the wild and captive François' langurs. Similarly, the proportion of Bacillota differed between the langur species, with a higher proportion in the white-headed langurs than the François' langurs. In addition, significant separation in gut microbiome functions also occurred between the two species. The functional genes related to metabolism (e.g., carbohydrate metabolism and amino acid metabolism) and Glycoside Hydrolases in wild François' langurs were more abundant than in the other langurs. The results of PCoA showed that the pathways were significantly separated between white-headed langurs and François' langurs at four levels in the KEGG database, whereas the pathways showed no significant differences between the wild and captive François' langurs except for module level. The proportion of ARGs related to multidrug resistance was higher in wild François' langurs, likely associated with the utilization of poultry manure and antibacterial biocides in the langur's habitat.

CONCLUSION: Our study demonstrates that the host-associated factors have stronger influence on shaping the gut microbiome of langurs than environmental factors. These findings provide data on the relative contributions of host-associated factors and environmental factors to the gut microbiome of langurs and identify potential driving factors for antibiotic resistance genes. In addition, these findings provide crucial insights into the influence of host-associated factors on the gut microbiome, offering a theoretical basis for future langur conservation strategies.},
}

@article {pmid42877015,
year = {2026},
author = {Gao, W and Han, W and Chen, J and Gao, Z and Gao, J and Zhen, R and Yuan, Y and Gu, Y and Huang, C and Liu, C and Wang, G and Zhang, X and Zhao, Z and Xiong, G and Li, X and Zhu, P and Liu, J and Hu, C and Gong, Y and Zhang, Z},
title = {Targeted next-generation sequencing: a promising approach for pathogen and antimicrobial resistance gene detection in urinary tract infections.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1945070},
pmid = {42877015},
issn = {1664-302X},
abstract = {OBJECTIVE: Urinary tract infections (UTIs) are common and frequently recurrent. As traditional diagnostic methods fail to meet clinical needs, this study aimed to construct and evaluate the performance of targeted next-generation sequencing (tNGS) for detecting pathogens and antimicrobial resistance genes (ARGs) in urine specimens.

METHODS: A total of 446 urine samples from patients with suspected UTIs were tested by tNGS, routine culture, and antimicrobial susceptibility testing (AST), with discordant results resolved by metagenomic NGS (mNGS) and whole-genome sequencing (WGS). The performance of tNGS was evaluated against culture and a composite reference standard (CRS) for pathogen detection, and against AST and WGS for resistance prediction.

RESULTS: tNGS achieved limit of detections of 500-1,000 CFU/mL, with high precision. Compared to culture, tNGS achieved a higher positive rate (62.78%), along with an overall sensitivity of 90.05% and specificity of 56.28%, whereas against the CRS the sensitivity and specificity reached 99.54% and 97.49%, respectively. For the seven common UTI bacteria, both metrics exceeded 90% regardless of the reference standard. Additionally, tNGS outperformed culture in detecting hard-to-culture microbes and polymicrobial infections. Among 132 samples with available AST results, ARG-based prediction showed strong concordance with resistance phenotypes for carbapenems (100.00%) and third generation cephalosporins + β-lactamase inhibitors (91.67%). Factors including sex and urine leukocyte count > 10 cells/μL were found associated with positive tNGS results.

CONCLUSION: tNGS enables rapid, sensitive and comprehensive detection of UTI pathogens and ARGs, covering hard-to-culture pathogens and mixed infections, thereby showing promise in improving diagnosis. However, it complements rather than replaces phenotypic AST, particularly for penicillin-class antibiotics.},
}

@article {pmid42877059,
year = {2026},
author = {Xue, Y and Cai, S and Ji, L and Ji, L and Shen, Q and Wang, X and Wu, P and Liu, Y and Wang, Y and Zhang, W and Yang, S},
title = {Identification and characteristics of multiple viruses in snow leopard fecal samples using viral metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1946718},
pmid = {42877059},
issn = {1664-302X},
abstract = {Metagenomic studies on the fecal virome of snow leopards, rare apex predators on the Qinghai-Tibet Plateau (QTP), remain limited. In this study, we utilized metagenomic sequencing to characterize the fecal viral community in captive QTP snow leopards. We assembled 22 complete viral genomes across the families Anelloviridae, Circoviridae, Parvoviridae, Picornaviridae, Genomoviridae, and Smacoviridae. Phylogenetic analyses indicated substantial sequence novelty. We identified 9 anellovirus genomes in the genera Tettorquevirus and Etatorquevirus, 3 candidate novel parvoviruses in Bocaparvovirus, Chaphamaparvovirus, and Dependoparvovirus, 3 circovirus genomes representing 2 candidate novel species, and 1 candidate novel sakobuvirus species. Another kobuvirus genome represented a divergent strain of a known species. In addition, 4 divergent genomoviruses showed phylogenetic relationships with sequences reported from diverse animal and environmental sources. Notably, one candidate novel porprismacovirus (family Smacoviridae) displayed a marked discordance between its highly conserved replication-associated protein (96.7% amino acid identity), divergent capsid protein (maximum identity, 59.7%), and low whole-genome identity (63.6%). Recombination analysis suggested it might be a recombinant virus. In summary, this study expands current knowledge of the diversity and evolutionary characteristics of viruses detected in snow leopard fecal samples and provides baseline genomic data for future investigation of captive snow leopard viromes.},
}

@article {pmid42877104,
year = {2026},
author = {Tang, H and Xiong, Q and Qian, G},
title = {Exploratory microbiota-metabolite alterations associated with cognitive impairment after repeated low-dose sevoflurane exposure in mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1869293},
pmid = {42877104},
issn = {2235-2988},
mesh = {Animals ; *Sevoflurane/adverse effects/administration & dosage ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cognitive Dysfunction/chemically induced/microbiology ; Mice, Inbred C57BL ; Metabolomics ; Disease Models, Animal ; Maze Learning/drug effects ; *Microbiota/drug effects ; *Metabolome/drug effects ; },
abstract = {BACKGROUND: Repeated low-dose sevoflurane exposure may affect cognition, but the relationship between such exposure, gut microbial composition, and circulating metabolites remains unclear. This study examined an experimental proof-of-concept exposure model and treated microbiota-metabolite findings as exploratory associations.

METHODS: Mice were exposed to 100 ppm sevoflurane for 2 h/day over 7 consecutive days, followed by Morris water maze testing without a long-term recovery follow-up. Gut microbiota and serum metabolites were profiled by shotgun metagenomic sequencing and LC-MS metabolomics, respectively, and machine-learning analyses were used only for exploratory feature ranking.

RESULTS: Sevoflurane-exposed mice exhibited poorer Morris water maze performance (Day 6 escape latency: 28.6 ± 3.4 s vs. 12.5 ± 1.8 s in controls, p < 0.01), although interpretation is limited by unequal behavioral sample sizes. Serum metabolomics suggested nominal and exploratory alterations in bile acid- and sphingolipid-related pathways. Shotgun metagenomics (n = 3/group) identified preliminary relative-abundance shifts, including a lower Bacteroidota/Bacillota ratio and lower relative abundance of Akkermansia.

CONCLUSIONS: In this proof-of-concept model, repeated low-dose sevoflurane exposure was associated with impaired spatial learning and memory and with exploratory serum metabolic and gut microbial alterations. The findings do not establish persistent long-term deficits, routine occupational risk, or causal microbiota-metabolite mediation. Larger cage-aware studies, an ambient-air comparison group, targeted validation, and interventional experiments are required.},
}

Animals
*Sevoflurane/adverse effects/administration & dosage
Mice
Male
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Cognitive Dysfunction/chemically induced/microbiology
Mice, Inbred C57BL
Metabolomics
Disease Models, Animal
Maze Learning/drug effects
*Microbiota/drug effects
*Metabolome/drug effects

@article {pmid42877189,
year = {2026},
author = {},
title = {Correction: Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag274},
doi = {10.1093/ismeco/ycag274},
pmid = {42877189},
issn = {2730-6151},
abstract = {[This corrects the article DOI: 10.1093/ismeco/ycag081.].},
}

@article {pmid42877214,
year = {2026},
author = {Kalendar, R and Daniyarov, A and Kairov, U and Kozhakhmetov, S and Yerezhepov, D and Yermekbayeva, B and Sarbassov, D and Kushugulova, A},
title = {Targeted long-read eukaryotic profiling of human stool by broad-range 18S-28S rRNA gene amplicon sequencing on Oxford Nanopore Technologies: a proof-of-concept study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1904425},
pmid = {42877214},
issn = {1664-302X},
abstract = {The gut eukaryome, comprising the protists and fungi that fall within the strict definition of the microbiota together with the macroscopic helminths and arthropods that lie outside it, is under-detected by clinical microscopy and by short-read 16S/18S sequencing, yet is increasingly implicated in inflammatory and autoimmune disorders, including psoriasis. Existing 18S V4/V9 primers either lack cross-kingdom universality or fail to discriminate closely related species. We designed and evaluated broad-range PCR primers anchored in conserved blocks of nuclear 18S and 28S ribosomal genes, flanking a 1.0-3.5 kb cassette spanning the 3'-end of 18S, ITS1, 5.8S, ITS2, and the 5'-end of 28S. Stool samples from 91 plaque-psoriasis patients and 92 matched controls were collected; a subset of 32 samples was profiled by Oxford Nanopore amplicon sequencing using the EPI2ME wf-metagenomics pipeline (Kraken + Bracken) against the NCBI core_nt database. The gut eukaryome was dominated by Ascomycota and Protista, with 51 species-level entries assigned to Candida (37 named binomials), 27 entries assigned to Blastocystis (12 subtype-labelled entries), 20 entries assigned to Malassezia (15 named species), and 37 entries assigned to Cladosporium recovered from a single PCR tube. Blastocystis hominis was detected in 37.5% of subjects (≥50-read threshold; mean 7.5% in carriers), with concurrent detection of 12 subtype-labelled entries (ST1-ST4, ST7, ST10-ST15, ST24) and 11 named isolate entries. Psoriasis-relevant Candida species, such as C. albicans (34.4%), C. tropicalis (34.4%), C. parapsilosis (31.2%), and Malassezia restricta (9.4%; up to 12.1%) were co-detected. Long-read sequencing of a broad-range 18S -28S rRNA gene cassette provides a single-tube workflow for the simultaneous recovery of fungal, protistan, and plant-derived eukaryotic sequences from human stool.},
}

@article {pmid42877526,
year = {2026},
author = {Fang, YH and Liu, HN and Chen, YJ and Hsu, TW and Chiu, CA and Chiang, PN and Huang, CL},
title = {Metagenomic profiling reveals that divergent fire-adaptive strategies drive distinct fungal succession in pine litter decomposition.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201414},
pmid = {42877526},
issn = {2210-6340},
abstract = {Decomposing litter is a critical driver of fuel bed formation and forest fire regimes, yet how divergent plant fire-adaptive strategies influence litter chemistry and subsequent fungal decomposition dynamics remains poorly understood. Here, we conducted a 6-month reciprocal litterbag experiment by incubating litter from two contrasting pine species-the fire-tolerant Pinus taiwanensis and the fire-avoiding P. morrisonicola-in both their own native habitat and that of the other species, coupled with genome-resolved metagenomics to track fungal succession and lignocellulolytic functional profiles. We found that the fire-avoiding P. morrisonicola exhibited significantly accelerated decomposition, driven by inherently lower initial C:N ratio and less recalcitrant litter, whereas the fire-tolerant P. taiwanensis exhibited slower decomposition rates. Metagenomic profiling revealed a distinct functional succession underlying this process. Early decomposition was dominated by Ascomycota (e.g., Leotiomycetes), which rapidly colonized the litter to initiate biopolymer breakdown. As easily decomposable substrates depleted, a functional shift occurred. Specifically, the highly recalcitrant P. taiwanensis litter selectively recruited Basidiomycota (e.g., Agaricales and Trechisporales) equipped with diverse lignin-modifying enzymes, reflected by a late-stage temporal surge in ligninolytic gene abundances. Ultimately, these findings demonstrate that plant fire-adaptive strategies act as a strong filter, shaping litter chemistry to drive specific taxonomic and functional fungal succession. This study provides a mechanistic understanding of the eco-evolutionary linkage between plant traits, microbiome assembly, and ecosystem-level fire dynamics.},
}

@article {pmid42877629,
year = {2026},
author = {Metzler-Zebeli, BU and Balfanz, F and Vollrath, F},
title = {Fibrolytic capacity of the gut microbiome in captive African elephants (Loxodonta africana): a pilot study.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1933152},
pmid = {42877629},
issn = {2297-1769},
abstract = {African elephants (Loxodonta africana) depend on the fibrolytic capacity of their gut microbiome (GMB) to efficiently utilize fibrous plant material. However, knowledge is missing on the temporal stability and functional dynamics (especially fibrolytic capacity) of their GMB. Likewise, information on the associated volatile fatty acids (VFA) production in the elephant's hindgut is scarce. In this pilot study, we collected feces from five captive African elephants on two occasions separated by 12 months to explore the GMB composition and its changes over time. We characterized the GMB's fibrolytic potential based on total microbial numbers and metagenome composition, including carbohydrate-active enzymes (CAZy), and fecal VFA, at individual and group level. Elephants received a roughage-based diet, which contained more carrots at the second than at the first sampling. Bacteria, specifically fibrolytic Prevotella, Bacteroides, Ruminococcus and Fibrobacter dominated the GMB, while archaea, fungi and protozoa were less present. Treponema was highly abundant, which might be an adaptation to maximize energy gain from cellulose-rich food. The elephants showed individual shifts in GMB composition from the first to second sampling. The shift in functional gene composition from the first to the second sampling was similar among elephants. It showed distinct clustering of CAZy families between fecal collections and discriminated features related to breakdown of carrot pectin for the second sampling. Sparse partial least squares-discriminant analysis identified (hemi-)cellulolytic genera within Prevotellaceae as discriminant taxa, which positively associated with CAZy families but negatively with VFA. At group level, fecal VFA concentrations were similar among elephants. However, opposite shifts from the first to the second sampling were detected among elephants at individual level. It may be speculated whether feeding decisions of three related females might explain the increase of VFA in their feces at the second compared to the first sampling, whereas VFA were lower in feces of the non-related female at the second sampling. We assert that this pilot study on GMB taxonomy and carbohydrate breakdown in captive African elephants may be helpful for feeding management at zoological gardens.},
}

@article {pmid42878130,
year = {2026},
author = {Lamarca, AP and Silveira, MC and Azevedo, RC and Guimarães, MAAM and de Mello, CMB and Camargo, AC and de Souza, LM and Gerber, AL and Guimarães, APC and Cavalcanti, AC and Vasconcelos, ATR},
title = {First Phylodynamic Analysis of HRSV-A and HRSV-B in Rio de Janeiro, Brazil, Reveals Recurrent Dispersals From the Megalopolis Center to Suburban Cities.},
journal = {Journal of medical virology},
volume = {98},
number = {10},
pages = {e71177},
doi = {10.1002/jmv.71177},
pmid = {42878130},
issn = {1096-9071},
support = {E-26/210.717/2025//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; SEI260003/001621//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/200.095/2026//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 00x0ma614//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil/ ; },
mesh = {Brazil/epidemiology ; Humans ; *Phylogeny ; *Respiratory Syncytial Virus Infections/epidemiology/virology/transmission ; Genetic Variation ; Cities/epidemiology ; *Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification ; Female ; Infant ; Genome, Viral ; Respiratory Tract Infections/virology/epidemiology ; },
abstract = {Human respiratory syncytial virus (HRSV) is the leading cause of acute lower respiratory tract infections in infants and represents a major burden to public health systems worldwide. Despite its epidemiological relevance, genomic surveillance of HRSV in Brazil remains limited. Here, we investigated the genetic diversity and dispersal dynamics of HRSV-A and HRSV-B in the state of Rio de Janeiro, Brazil, during the period immediately preceding the implementation of maternal vaccination and prophylactic monoclonal antibodies. A total of 136 near-complete HRSV genomes were recovered from respiratory samples collected between May 2024 and June 2025 using metagenomic sequencing. Phylogenetic analyses identified 11 HRSV-A and five HRSV-B lineages, with most sequences belonging to the A.D.3 and B.D.E.1 clades. Phylodynamic reconstructions revealed multiple independent introductions into the state, with the city of Rio de Janeiro acting as the primary within-state dispersal hub. Viral dispersal routes originating from the capital also showed greater mean transmission distances than those from other municipalities. Coinfections with additional respiratory viruses were frequently detected, and most HRSV-positive patients were children under 1 year of age. These results demonstrate that HRSV circulation in Rio de Janeiro is shaped by repeated introductions and strong spatial structuring centered around highly connected urban areas. Our findings underscore the importance of continuous genomic surveillance to monitor viral evolution, characterize transmission dynamics, and support science-based public health strategies against HRSV. Establishing robust monitoring systems will be critical to evaluate the impact of newly implemented immunization programs in Brazil.},
}

Brazil/epidemiology
Humans
*Phylogeny
*Respiratory Syncytial Virus Infections/epidemiology/virology/transmission
Genetic Variation
Cities/epidemiology
*Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification
Female
Infant
Genome, Viral
Respiratory Tract Infections/virology/epidemiology

@article {pmid42878177,
year = {2026},
author = {Vliex, LMM and Godinho Mimoso, IF and Le, GN and Blaak, EE and Penders, J},
title = {Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746814},
doi = {10.1080/19490976.2026.2746814},
pmid = {42878177},
issn = {1949-0984},
mesh = {Humans ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Vancomycin/administration & dosage/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Obesity/microbiology/drug therapy ; *Trisaccharides/administration & dosage ; Double-Blind Method ; *Overweight/microbiology/drug therapy ; Female ; Adult ; Male ; Middle Aged ; Prebiotics/administration & dosage ; Feces/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotics are widely used to treat bacterial infections, yet overuse and misuse causes disruption of the gut microbiome and spread of antibiotic-resistant bacteria. Presence of antibiotic resistance genes (ARGs) could be a determinant of the response to antibiotics. Supplementation with prebiotics may limit the detrimental antibiotic-induced effects on the microbiome, but whether this results in changes in the gut resistome is unclear. This study investigated the impact of eight-week 2'-fucosyllactose (2'-FL) supplementation after seven-day vancomycin use in 18 adults with overweight/obesity, a subset from a double-blind placebo-controlled randomized intervention. Whole-metagenome shotgun sequencing was used to characterize the gut microbiome and resistome at baseline, after vancomycin use and after supplementation. Seven-day vancomycin use disrupted microbial richness and diversity (p < 0.001) and changed microbial composition. No improvements in microbial recovery were detected after eight week 2'-FL supplementation compared to placebo. Resistome richness and diversity were not affected by vancomycin use, although the presence of specific ARGs changed. No differential impact of 2'-FL supplementation on resistome richness, diversity and composition was detected. While vancomycin use disrupted the gut microbiome and affected the resistome, the detectable effects of 2'-FL supplementation were limited. Future research should investigate antibiotic- and prebiotic-induced changes in the gut resistome in more detail.},
}

Humans
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Vancomycin/administration & dosage/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Obesity/microbiology/drug therapy
*Trisaccharides/administration & dosage
Double-Blind Method
*Overweight/microbiology/drug therapy
Female
Adult
Male
Middle Aged
Prebiotics/administration & dosage
Feces/microbiology
Drug Resistance, Bacterial

@article {pmid42878179,
year = {2026},
author = {Shin, MG and Park, SJ and Kang, W and Bae, Y and Kim, S and Yoo, D and Yoon, S and Park, SM and Kwon, ES and Chang, J and Yoon, JH and Park, DG and Lee, EJ},
title = {Escherichia coli hns and methylglyoxal link gut microbial metabolism to host neuronal gene regulation in Parkinson's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2739674},
doi = {10.1080/19490976.2026.2739674},
pmid = {42878179},
issn = {1949-0984},
mesh = {Animals ; *Parkinson Disease/metabolism/microbiology/genetics ; Humans ; *Escherichia coli/metabolism/genetics ; Caenorhabditis elegans/genetics/microbiology ; *Gastrointestinal Microbiome ; *Pyruvaldehyde/metabolism/blood ; Dopaminergic Neurons/metabolism ; *Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation ; Male ; Disease Models, Animal ; Female ; Neurons/metabolism ; Feces/microbiology ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra (SN). Although the gut microbiota has been implicated in PD pathogenesis, how defined bacterial genes and their metabolites influence host neuronal gene regulation remains unclear. Here, we identify a gut microbial hns-methylglyoxal (MG) pathway linking Escherichia coli (E. coli) metabolism to host neuronal gene regulation. In the stool metagenomic cohort, hns, a bacterial gene encoding the histone-like nucleoid structuring protein and primarily derived from E. coli, was enriched particularly in body-first PD, a subtype associated with gut-originating pathology. In a separate plasma MG cohort, plasma levels of MG, a reactive metabolite whose bacterial production was hns-dependent in our model system, were higher in body-first than in brain-first PD and were nominally inversely associated with cardiac meta-iodobenzylguanidine (MIBG) uptake within the body-first group. Using Caenorhabditis elegans (C. elegans) PD models, we found that feeding with Δhns E. coli protected dopaminergic neurons, whereas exogenous MG abolished this neuroprotection. Transcriptomic and neuronal RNAi analyses identified rig-5 as a host mediator of hns deletion-induced neuroprotection. Cross-species analyses identified LSAMP as a candidate mammalian ortholog of rig-5. MG suppressed LSAMP expression in human neuronal cells, and LSAMP expression was reduced in the post-mortem SN of patients with PD. Conversely, Lsamp expression was increased in the SN of mice colonized with Δhns E. coli. Together, these findings delineate a microbial gene-metabolite-host gene pathway through which E. coli hns and MG modulate rig-5-dependent dopaminergic vulnerability in C. elegans, with corresponding changes of LSAMP expression in mammalian systems.},
}

Animals
*Parkinson Disease/metabolism/microbiology/genetics
Humans
*Escherichia coli/metabolism/genetics
Caenorhabditis elegans/genetics/microbiology
*Gastrointestinal Microbiome
*Pyruvaldehyde/metabolism/blood
Dopaminergic Neurons/metabolism
*Escherichia coli Proteins/metabolism/genetics
Gene Expression Regulation
Male
Disease Models, Animal
Female
Neurons/metabolism
Feces/microbiology

@article {pmid42878386,
year = {2026},
author = {Vojtková, M and Baltušis, M and Martiny, HM and Baral, A and Pyrounakis, N and Beleon, A and Freitag, R and Pico-Tomàs, A and Kaas, RS and Petersen, TN and Munk, P},
title = {PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag776},
pmid = {42878386},
issn = {1367-4811},
abstract = {MOTIVATION: Antimicrobial resistance databases are central to genomic surveillance, but resistance determinants remain distributed across resources with different scopes, structures, and annotations.

RESULTS: We developed PanRes, a curated resistance database of 11 717 genes integrating acquired and latent determinants of antibiotic, biocide, and metal resistance within a unified ontology. We predicted representative protein structures and clustered them by structural similarity, grouping proteins into 505 high-confidence structurally conserved clusters coherent despite sequence divergence. Their structure-guided alignments were used to build Hidden Markov Models (HMMs) for remote homology search. In seven wastewater metagenomes from five European cities, PanRes 3D-based HMMs expanded detection beyond what was possible with BLAST, with 35.3% of retained hits identified only by the HMMs and generally showing greater divergence from known proteins. For beta-lactamases, several proteins retained beta-lactamase-like folds and catalytic geometry despite weak sequence similarity.

PanRes is available through an interactive web platform (https://panres.rambio.dk/), a structure-informed resource for exploring the whole resistome. The database, HMM profiles, and ontology are available at Zenodo (10.5281/zenodo.22876216).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42878464,
year = {2026},
author = {Gonzalez, C and Ali, J and Román-Reyna, V and Vasco-Correa, J},
title = {Metagenome-assembled genomes from methane-fed bottle incubations under variable moisture and pH conditions.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0104126},
doi = {10.1128/mra.01041-26},
pmid = {42878464},
issn = {2576-098X},
abstract = {Methane-oxidizing microorganisms mitigate methane emissions in natural and engineered environments. We report 63 metagenome-assembled genomes recovered from methane-fed compost incubations under contrasting moisture and pH conditions, including 62 bacterial metagenome-assembled genomes (MAGs) and 1 archaeal MAG. The MAGs include methanotrophs and microorganisms involved in complementary carbon, nitrogen, sulfur, and carbohydrate metabolic functions.},
}

@article {pmid42878705,
year = {2026},
author = {Keuschnig, C and Feord, H and Broadwell, ELM and Zervas, A and Tranter, M and Anesio, AM and Benning, LG},
title = {Aerobic anoxygenic phototrophs are widespread and active members of Greenland Ice Sheet microbiomes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag116},
pmid = {42878705},
issn = {1574-6941},
abstract = {The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs), known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.},
}

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42879864,
year = {2026},
author = {Scott, WT and Jácome, LAP and Nijsse, B and Wang, J and Stouten, GR and Koehorst, JJ and Smidt, H and Edwards, EA and Schaap, PJ and Kleerebezem, R},
title = {Resolving metabolic interdependencies during chlorobenzene dechlorination in a Dehalobacter-containing community.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127036},
doi = {10.1016/j.watres.2026.127036},
pmid = {42879864},
issn = {1879-2448},
abstract = {Chlorinated benzenes are persistent groundwater contaminants whose anaerobic transformation can depend on organohalide-respiring microorganisms embedded within metabolically interconnected communities. Here, we asked which microorganisms and metabolic functions characterize a Dehalobacter-containing dechlorinating community, and whether bioinformatics and genome-resolved metabolic modeling could identify candidate interactions supporting organohalide respiration. To address these questions, we integrated dechlorination data from related Dehalobacter-containing enrichment lineages with genome-resolved metagenomics and constraint-based modeling. Transformation of 1,2,4-trichlorobenzene (TCB) to dichlorobenzenes and monochlorobenzene (MCB) was observed in one enrichment lineage, whereas MCB transformation to benzene was observed in a related lineage; in the latter, benzene increased from 0 to 62.3μmol bottle[-1] as MCB decreased from 88.3 to 22.0μmol bottle[-1] over 120 days. These experiments comprised one observation unit per lineage rather than independent biological reactor replicates and therefore do not establish continuous TCB-to-benzene conversion within a single culture. Genome-resolved reconstruction identified two Dehalobacter populations among 12 community members selected for metabolic modeling. Following structural, phenotypic, and thermodynamic quality control, pairwise random flux sampling predicted a metabolically differentiated exchange network: Methanobacterium consumed H2 in all 11 pairwise models (median model-normalized flux, 22.36 mmol gDW[-1] h[-1]), whereas Methanothrix consumed acetate in all 11 (10.16 mmol gDW[-1] h[-1]) and released CH4 (9.51 mmol gDW[-1] h[-1]), distinguishing hydrogenotrophic and acetoclastic methanogenic functions. Model-guided community reduction across 39 sensitivity scenarios produced objective-minimal candidate communities in 34 scenarios, predominantly bicultures with condition-dependent recruitment of a third member. A Dehalobacter member occurred in every candidate community and Methanothrix recurred across all evaluated scenarios, defining a compact model-predicted Dehalobacter-methanogen backbone rather than demonstrating biological indispensability. Together, these results distinguish observed dechlorination from genome-inferred metabolic potential and model-predicted interactions, providing experimentally testable hypotheses for metabolic dependencies that could inform more predictable anaerobic bioremediation strategies.},
}

@article {pmid41603601,
year = {2026},
author = {Stairs, B and Johnson, H and Mondron, K and Syring, KC and Guerrero, A and Ballou, ER and King, JS and Pawlowska, TE and Adeleke, R and Stevens, DA and Uehling, JK},
title = {Genomic analyses of globally distributed Rhizopus microsporus populations indicate clinical isolates derived from environmental diversity reservoirs.},
journal = {Mycologia},
volume = {118},
number = {2},
pages = {316-329},
doi = {10.1080/00275514.2025.2594974},
pmid = {41603601},
issn = {1557-2536},
support = {NSF 2202410//National Science Foundation/ ; NSF 2030338//National Science Foundation/ ; BB/W002760/1//BBSRC/ ; },
mesh = {Humans ; *Disease Reservoirs/microbiology ; DNA, Environmental/genetics/isolation & purification ; DNA, Fungal/genetics/isolation & purification ; Genome, Fungal ; *Mucormycosis/microbiology ; Polymorphism, Single Nucleotide ; *Rhizopus/genetics/isolation & purification ; *Soil Microbiology ; Whole Genome Sequencing ; Metagenomics ; },
abstract = {Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is Rhizopus microsporus, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)-based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six R. microsporus isolates and combined these data with publicly available whole genome sequences of 46 R. microsporus isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus Mycetohabitans (Burkholderiales). Lastly, we observed that genome assembly size in R. microsporus is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of Rhizopus and related fungi that cause mucormycosis.},
}

Humans
*Disease Reservoirs/microbiology
DNA, Environmental/genetics/isolation & purification
DNA, Fungal/genetics/isolation & purification
Genome, Fungal
*Mucormycosis/microbiology
Polymorphism, Single Nucleotide
*Rhizopus/genetics/isolation & purification
*Soil Microbiology
Whole Genome Sequencing
Metagenomics

@article {pmid42868942,
year = {2026},
author = {Shu, W and Wang, P and Yang, J and Ding, M and Qin, L and Huang, G and Zhang, H and Ge, Y},
title = {Linking microbial community reassembly to multi-element metabolic potential across community and genome scales in rivers impacted by ion-adsorption rare earth mining.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127131},
doi = {10.1016/j.watres.2026.127131},
pmid = {42868942},
issn = {1879-2448},
abstract = {Ion-adsorption rare earth element (REE) mining can create a composite pollution environment characterized by acidification and enrichment of NH4[+], SO4[2][-], and REEs, yet its effects on riverine microbial community assembly and multi-element metabolic potential remain poorly understood. Here, we combined 16S rRNA amplicon sequencing, metagenomic sequencing, and metagenome-assembled genomes (MAGs) to characterize microbial community assembly and functional reorganization across a mining-disturbance gradient. At the community level, bacterial and archaeal richness and diversity declined significantly with increasing pollution, accompanied by clear community differentiation. Compared with bacteria, archaea exhibited greater environmental specificity, with larger contributions of homogeneous selection and dispersal limitation to community assembly. Meanwhile, microbial functional genes formed a modular network linking carbon, nitrogen, sulfur, iron, arsenic, and methane transformation processes, with particularly prominent cross-module associations among carbon-, nitrogen-, and sulfur-related functions. At the genome level, mining-associated MAGs showed multifunctional integration within individual genomes and potential functional division of labor and complementarity among different microbial members. Together, the community- and genome-level results revealed a cross-scale organization of multi-element metabolic potential, extending from functional network connectivity at the community level to functional configuration at the genome level. Such mining-driven reorganization of microbial communities and metabolic functions may further influence greenhouse-gas-related processes and the mobility and transformation of metal(loid)s, providing new insights into microbial ecological processes and potential ecological risks in mining-impacted rivers.},
}

@article {pmid42868958,
year = {2026},
author = {Yan, C and Liu, J and Ma, S and Cheng, Z and Xu, H and Shangguan, YX and Liu, H},
title = {Rhizosphere functional microbiome remodeling by Streptomyces and jasmonic acid mitigates cadmium accumulation in rice.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128761},
doi = {10.1016/j.micres.2026.128761},
pmid = {42868958},
issn = {1618-0623},
abstract = {Cadmium (Cd) contamination poses a serious threat to rice production and food safety because of its high mobility in soil and its accumulation in edible rice tissues. Although beneficial microorganisms and plant signaling regulators have individually shown potential for alleviating Cd stress, whether their combined application can reduce Cd accumulation by restructuring rhizosphere microbial functions remains poorly understood. This study investigated the effects of two Cd-tolerant, plant growth-promoting Streptomyces strains, alone or in combination with jasmonic acid (JA), on Cd stress, Cd accumulation, and rhizosphere microbial communities and functions in rice. The results indicated that Streptomyces co-inoculation improved rice growth, photosynthetic performance, antioxidant defense, and osmotic regulation. It also reduced soil Cd bioavailability and altered Cd partitioning within rice plants. JA alone exerted relatively limited effects on the rhizosphere microbiome but strengthened Streptomyces-mediated physiological and microbial responses when applied in combination. Metagenomic analysis showed that the treatments altered microbial community composition and enriched COG functions associated with inorganic ion transport, signal transduction, and cell envelope biogenesis. KEGG analysis further revealed changes in pathways associated with environmental sensing and Cd detoxification, particularly the two-component system and glutathione metabolism. BacMet analysis identified 37 Cd-related resistance genes. Streptomyces co-inoculation broadly enriched resistance modules involved in metal sensing, transport, efflux, and detoxification, whereas the combined treatment selectively enriched core resistance genes, including czcA, czcP, zntA, and nccB. These changes were consistent with the reduced bioavailable Cd in rhizosphere soil and lower Cd accumulation in rice. Rather than increasing the number of responsive genes, the addition of JA to Streptomyces co-inoculation was associated with a more focused Cd resistance gene response, particularly involving metal transport and efflux. Overall, the reduction in Cd accumulation was associated with coordinated changes in rhizosphere microbial communities, metabolic pathways, and Cd resistance genes. These findings highlight the potential of combining Streptomyces co-inoculation with JA as a microbiome based strategy for rice cultivation in Cd contaminated soils.},
}

@article {pmid42869245,
year = {2026},
author = {Ríos-Castro, R and Allen, A and Itoh, N and Long, A and Bower, S and Joseph, A and Kim, E and Collins, C and Wickramanayaka, DN and Lynch, S and Culloty, S and Hill, R and Bignell, J and Green, M and Ward, GM and Tidy, A and Kerr, R and White, P and Cano, I},
title = {Surveillance, genetic diversity, and virulence characterisation of Francisella halioticida in blue mussels from the United Kingdom and Ireland.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108763},
doi = {10.1016/j.jip.2026.108763},
pmid = {42869245},
issn = {1096-0805},
abstract = {Francisella halioticida is a recently recognized pathogen affecting molluscs. In Europe, its presence has been documented within mussel populations in both France and England. At present, data concerning its genetic variability in mussels remain scarce. Between 2024 and 2025, a comprehensive monitoring programme was implemented to assess F. halioticida prevalence in southern England, alongside analyses of archived samples from Scotland and Ireland. The findings indicated a low prevalence of the pathogen within the surveyed populations, primarily associated with mild or localized infections. Phylogenetic analyses based on multi-locus sequence analysis showed genetic variability of F. halioticida in mussels across surveyed locations and years, however a distinct F. halioticida cluster from mussels separated from F. halioticida infecting scallops and abalone was identified. A F. halioticida metagenome assembled genome was obtained from an infected mussel from southern England, with 3666 predicted ORFs, and a ~14.2 kb region containing a putative Francisella Pathogenicity Island, including genes associated with Type VI secretion system components (TssK, DotU, IglE, and IglH), together with several hypothetical proteins, and flanked by IS3 family transposases. Additional virulence-associated genes were detected, including transcriptional and global regulators, oxidative stress and detoxification genes, and metallopeptidases. These findings improve understanding of the occurrence, diversity, and genomic features of F. halioticida in wild mussel populations, highlighting the need for expanded surveillance and higher-resolution genomic data to better understand its epidemiology and pathogenic potential. This improved resolution enhances risk assessment, enables early detection of emerging lineages, and supports more targeted monitoring strategies for wild mussel populations.},
}

@article {pmid42869256,
year = {2026},
author = {Pan, LL and Liang, W and Ren, Z and Yang, J and Jia, K and Wang, Q and Ma, Y and Tian, H and Zou, H and Liu, H and Wang, L and Wu, M and Li, B and Yang, S and Zuo, J and Wang, Z and Yang, Q and Dong, X and Bhatia, M and Peng, S and Zhou, C and Zou, WB and Liao, Z and Zou, D and Diana, J and Sun, J},
title = {HtpG-High-Expressing Escherichia coli Promotes Fibrosis in Chronic Pancreatitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.025},
pmid = {42869256},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Chronic pancreatitis (CP) is a progressive fibroinflammatory disease with rising global incidence and no curative therapy. Gut dysbiosis has been associated with CP, but its causal contribution to disease pathogenesis remains unclear. We intended to identify specific pathogenic microbial species that promote CP and to delineate the underlying pathogenic mechanisms.

METHODS: Multi-omics analyses were used to identify key microbial signatures in CP patients and mice. Novel pathogenic Escherichia coli strains were isolated and bioengineered for functional studies. In vitro and in vivo assays, along with macrophage-specific knockout mice, adenoviral tools, and pharmacological inhibitors, were employed to dissect host-microbe mechanistic pathways. Therapeutic intervention included administering a screened next-generation probiotic.

RESULTS: Metagenomic sequencing identified HtpG-high-expressing E. coli (HHEC) enrichment as a dominant microbial signature in CP patients. Prevention of HHEC adherence and colonization alleviated CP, whereas recolonization with a new patient-derived HHEC strain PS718 exacerbated it. Mechanistically, E. coli-derived HtpG upregulated protein arginine methyltransferase 5 (PRMT5) in pancreatic macrophages. Pharmacological inhibition of PRMT5 or macrophage-specific deletion of PRMT5 mitigated pancreatic fibrosis and CP progression. PRMT5 methylated Krüppel-like factor 4 (KLF4) at residues R387/R389, stabilizing it, which promoted M2 polarization and pancreatic fibrosis. Therapeutic intervention with Akkermansia muciniphila, which is reduced in CP, suppressed HHEC colonization and ameliorated CP.

CONCLUSION: These findings provide novel evidence for a pathogenic HHEC-HtpG-macrophage axis in CP, highlighting the potential of microbiota-targeted therapies for the condition.},
}

@article {pmid42869338,
year = {2026},
author = {Tao, C and Wan, K and Song, Y and Xu, X and She, M and Sun, Z and Zhu, J and Yu, Y},
title = {Parsing the relationships among gut microbiome, neurotransmitter metabolome, glymphatic function, and cognition across healthy elderly, mild cognitive impairment, and probable Alzheimer's disease.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107067},
doi = {10.1016/j.bbi.2026.107067},
pmid = {42869338},
issn = {1090-2139},
abstract = {BACKGROUND: Evidence has suggested brain glymphatic dysfunction and gut microbial metabolic disturbance in Alzheimer's disease (AD), yet the relationships among gut microbiota, neurotransmitter metabolites, glymphatic function, and cognition across clinically defined groups of healthy elderly, mild cognitive impairment (MCI), and probable AD remain unclear.

METHODS: Using metagenomic sequencing, targeted metabolomics, and multi-modal magnetic resonance imaging, we measured the gut microbiome, neurotransmitter metabolome, and a variety of glymphatic markers in 30 patients with clinically diagnosed probable AD, 75 individuals with MCI, and 59 healthy controls (HC).

RESULTS: Although global microbial diversity showed no group difference, MCI and AD showed shared and unique species-level microbial alterations relative to HC. Despite the absence of overall metabolomic divergence, AD exhibited reduced levels of multiple neurotransmitter metabolites compared with MCI and HC. Prominent alterations in multiple glymphatic markers were present in AD rather than in MCI. Further integrated analyses revealed a wide range of associations among these multi-omics changes and established potential serial mediation pathways, manifesting as a pattern of gut microbiota → neurotransmitter metabolites → glymphatic function → cognition.

CONCLUSIONS: These findings could enrich our understanding of the biological mechanisms involved in cognitive impairment and clinically diagnosed probable AD, but also may inform future preventive and therapeutic interventions by targeting the established pathways.},
}

@article {pmid42869367,
year = {2026},
author = {Wang, J and Liu, H and Zhang, D and Wang, H and Jin, H and Yan, H},
title = {Enhanced remediation of wastewater impacted by acid mine drainage at low temperature using sulfate-reducing bacteria immobilized in biomass-amended PVA-SA beads.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125903},
doi = {10.1016/j.envres.2026.125903},
pmid = {42869367},
issn = {1096-0953},
abstract = {Acid mine drainage (AMD) is a severe environmental threat owing to its high acidity, sulfate, and heavy metal content with devastating effects on watershed ecosystems. In cold-climate mining regions, water temperature below 15 °C severely limits conventional bioremediation, as most functional bacteria are mesophilic. In this study, we tested the hypothesis that sulfate-reducing bacteria (SRB) capable of AMD remediation persist in cold mine environments and that their activity can be enhanced via gradient cold acclimation. Indigenous functional consortia were enriched and acclimated from AMD-contaminated sediments collected in the Shandi River basin, China. Metagenomic analysis confirmed the dominance of Desulfovibrio, the presence of complete dissimilatory sulfate reduction pathways, alongside cold-adaptation and acid-tolerance genes. Free-living cells were then immobilized in polyvinyl alcohol-sodium alginate (PVA-SA) beads containing corn straw pretreated with raw AMD. The results demonstrated that the beads possessed a porous network structure and enabled sustained carbon source release, attaining a sulfate removal efficiency of 98.5% in synthetic mining wastewater (SMW) at 12 °C. Solid-phase characterization verified that sulfate and heavy metals were transformed into stable crystalline phases. Furthermore, Microbial community profiling revealed that fermentative bacteria dominated the consortium, which could convert straw into bioavailable substrates that sustained SRB metabolism. These results demonstrated that immobilized bacteria were potentially and practically applied to AMD-impacted wastewater remediation despite the cold climate.},
}

@article {pmid42869479,
year = {2026},
author = {Iervolino, M and Günther, A and Schuele, L and Soto, F and Leijten, L and Bestebroer, TM and Coerper, A and Reade, A and Wallis, B and Lisovski, S and Leotta, G and Beer, M and Dewar, M and Kuiken, T and Begeman, L and Vanstreels, RET},
title = {Avian cholera causes mass mortality at penguin mega-colonies amid H5N1 HPAI outbreaks in Antarctica.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2080},
pages = {},
doi = {10.1098/rspb.2026.1271},
pmid = {42869479},
issn = {1471-2954},
support = {//International Association of Antarctica Tour Operators (IAATO)/ ; //Ocean Expeditions/ ; 101 084 171//European Union/ ; },
mesh = {Animals ; Antarctic Regions/epidemiology ; *Pasteurella multocida/isolation & purification/genetics ; *Spheniscidae ; *Disease Outbreaks/veterinary ; *Pasteurella Infections/veterinary/mortality/epidemiology/microbiology ; *Influenza A Virus, H5N1 Subtype/physiology ; *Influenza in Birds/mortality/epidemiology/virology ; Phylogeny ; },
abstract = {The characterization of pathogens affecting Antarctic wildlife has been historically limited and sporadic. With the introduction of H5N1 high pathogenicity avian influenza virus (HPAIV) in Antarctica in the austral summer 2023/2024, concerns about the health of Antarctic seabirds and mammals prompted immediate surveillance efforts. In March 2024, we visited the Danger Islands archipelago, that hosts two mega-colonies of Adélie penguins, and observed an unusual mortality estimated in thousands of Adélie penguins and other species. Swabs and tissues were collected for molecular detection of infectious agents from 49 carcasses, and additional tissues for histology from a selection of 9 carcasses. We detected Pasteurella multocida DNA in 46 of 49 individuals, and diagnosed avian cholera as the cause of death of most of these animals. By shotgun sequencing, we retrieved the first genomic sequences of the P. multocida strain from this region, and the phylogenetic analysis showed a close relation with strains from other locations retrieved during the same expedition and with strains previously reported in the Southern Ocean area. This study confirms avian cholera as a relevant cause of mortality in the Antarctic, and overall highlights the importance of considering this disease in the differential diagnoses during mortality events in Antarctica.},
}

Animals
Antarctic Regions/epidemiology
*Pasteurella multocida/isolation & purification/genetics
*Spheniscidae
*Disease Outbreaks/veterinary
*Pasteurella Infections/veterinary/mortality/epidemiology/microbiology
*Influenza A Virus, H5N1 Subtype/physiology
*Influenza in Birds/mortality/epidemiology/virology
Phylogeny

@article {pmid42869831,
year = {2026},
author = {Li, T and Song, ZX and Yang, DM and Ren, GX and Yin, Y and Yan, YG and Gao, J and Jiang, D and Liu, CS},
title = {[Diversity of endophytes in licorice from different habitats based on metagenomics and analysis of their correlation with accumulation of active ingredients].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {18},
pages = {5253-5261},
doi = {10.19540/j.cnki.cjcmm.20260415.406},
pmid = {42869831},
issn = {1001-5302},
mesh = {*Endophytes/genetics/classification/metabolism/isolation & purification ; *Glycyrrhiza/microbiology/chemistry/metabolism ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; Glycyrrhizic Acid/metabolism/analysis ; Biodiversity ; },
abstract = {Licorice is an important TCM. Its medicinal quality mainly depends on the accumulation of active ingredients such as flavonoids(such as liquiritin and isoliquiritin) and triterpenoids(such as glycyrrhizic acid), and the endogenous microbial community is considered an important environmental factor influencing the synthesis of these components. To analyze the regulatory effect of endophytes on secondary metabolites of licorice, metagenomic sequencing and ultra-high performance liquid chromatography were used to compare and analyze the composition and function of endophytes in wild and cultivated licorice roots as well as their relationship with the main active ingredients. The results showed that the content of liquiritin, isoliquiritin, and glycyrrhizic acid in wild licorice was significantly higher than that in cultivated licorice. The metagenomic analysis annotated that the endophytes in wild licorice belonged to 31 phyla and 315 genera, while those in cultivated licorice belonged to 24 phyla and 125 genera. Among them, Rathayibacter, Plantibacter, and other genera were significantly enriched in wild licorice, while only Lysobacter was significantly enriched in cultivated licorice. Functional annotations indicated that the endophytes in wild licorice were enriched in pathways such as two-component systems, nitrogen metabolism, and aminoacyl tRNA synthesis, while those in cultivated licorice were enriched in pathways such as photosynthesis and carbon fixation. Further correlation analysis revealed that some endophyte genera(such as Phenylobacterium and Microbacterium) and functional pathways(such as signal transduction and terpenoid metabolism) were significantly positively correlated with the content of glycyrrhizic acid and liquiritin. In addition, the abundance of glycosyltransferases and cytochrome P450 in endophytes in wild licorice was significantly higher than that in cultivated licorice. This indicated that they had an enzymatic basis for participating in the synthesis of host glycosides. This research systematically reveals the differences in endophytic community structure, function, and accumulation of active ingredients between wild and cultivated licorice, providing a theoretical basis for understanding the microbial mechanism of endophytes regulating the quality of licorice, and also offering references for developing microbial fertilizers to improve the quality of licorice.},
}

*Endophytes/genetics/classification/metabolism/isolation & purification
*Glycyrrhiza/microbiology/chemistry/metabolism
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
Glycyrrhizic Acid/metabolism/analysis
Biodiversity

@article {pmid42870288,
year = {2026},
author = {Wang, Y and Zhou, M and Malmuthuge, N and Chen, Y and Alexander, TW and Timsit, E and Guan, LL},
title = {Optimized approaches to profile low biomass DNA and RNA virome in the upper respiratory tract of beef cattle.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42870288},
issn = {2524-4671},
abstract = {BACKGROUND: Viruses play a key role in cattle respiratory tract (RT) health, yet, profiling the upper respiratory tract (URT) virome (DNA and RNA viruses) from deep nasopharyngeal swabs (DNS) remains challenging due to their low biomass, lack of well-defined enrichment approaches, and a high proportion of unclassified viral sequences. This study aimed to optimize DNS preservation, nucleic acid extraction, and bioinformatics pipelines to enhance URT virome characterization in beef calves.

RESULTS: Three DNS preservation methods were tested (RNAlater, brain heart infusion (BHI) medium/glycerol at -80 °C, and BHI medium/glycerol followed by RNAlater). Three nucleic acid extraction kits (QIAamp Fast DNA Stool Mini Kit, GeneJET Genomic DNA Purification Kit, and mirVana™ miRNA Isolation Kit) were evaluated to compare total nucleic acid yields. Viral DNA and RNA were extracted separately using the NucleoSpin Virus Kit, which was optimized for viral nucleic acid recovery. The DNS samples that preserved in RNAlater and extracted using the NucleoSpin Virus kit generated highest viral DNA (1.35 ± 0.12 µg) and RNA (1.57 ± 0.09 µg) (mean ± SEM) yields for metagenomics sequencing. Metagenomic sequencing and viral taxonomic assignment using Kraken2 and Kaiju, respectively showed that Kaiju allowed maximum exact matches for viral taxonomy assignment and provided high-resolution outputs for the profiling of cattle URT viromes.

CONCLUSION: The use of an optimized nucleic acid extraction method and Kaiju-based classification enhanced viral nucleic acid recovery and taxonomic classification from low-biomass DNS samples. The findings highlighted the importance of effective storage conditions and extraction methods in maximizing viral nucleic acid yield, while demonstrating that Kaiju provided more reliable viral taxonomic assignments than Kraken2. These advancements provide a framework for more accurate assessment of the URT virome in cattle and other farm animals, enabling deeper investigation into the roles of viruses in RT health.},
}

@article {pmid42870310,
year = {2026},
author = {Ren, G and Yang, T and Sheng, Z and Chen, Y and Chen, L and Wang, Y and He, P and Luo, H},
title = {Multi-omics reveals that dietary Piper sarmentosum Roxb. extract improves goat meat quality via the microbiota-muscle amino acid metabolic axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42870310},
issn = {1674-9782},
support = {2023YFD1600102//National Key R&D Program of China/ ; GHYF2022004//Key Research and Development Program of Hainan Province/ ; },
abstract = {BACKGROUND: Improving meat quality through nutritional regulation is an important approach in ruminant production. Growing evidence suggests that rumen microbiota influences host metabolism via microbial metabolites, thereby affecting meat quality. However, whether Piper sarmentosum Roxb. extract (PSE), a medicinal and edible plant-derived extract, improves meat quality through rumen microbiota-host metabolic interactions remains unclear. Thirty-six weaned male Hainan black goats (approximately 3 months old) were randomly assigned to four dietary treatments supplemented with 0, 200, 400, or 600 mg/kg PSE (dry matter basis), respectively. After a 90-day feeding trial, goats were fasted for 12 h before slaughter, and rumen and longissimus lumborum muscle samples were collected for subsequent analyses.

RESULTS: Supplementation with 600 mg/kg PSE significantly enhanced meat quality traits, including higher ultimate pH, improved color stability, and increased water-holding capacity, without affecting growth performance or carcass traits. Transcriptomic and metabolomic analyses revealed that PSE supplementation was associated with remodeling of amino acid and energy metabolism in muscle, particularly glutamate-related pathways. These metabolic changes were accompanied by increased expression of key metabolic genes, including BCAT2, IDH1, and IDH3A, alongside alterations in energy-related metabolites, such as the downregulation of carnitine and upregulation of creatinine. Concomitant shifts in rumen microbial composition were observed, with PSE supplementation increasing the abundance of genera like Weissella and Ruminococcus, while reducing potentially opportunistic genera, such as Acinetobacter and Klebsiella. Weissella showed strong positive correlations with elevated rumen metabolites like serine, threonine, choline, and hypoxanthine. Metagenome-assembled genome analysis of Weissella cibaria revealed an enrichment of genes related to amino acid metabolism and glycosyltransferase families. Correlation and mediation analyses further revealed associations among Weissella abundance, rumen metabolites, and muscle metabolic traits, supporting a potential microbiota-metabolite-host metabolic relationship.

CONCLUSIONS: Collectively, this study provides new insights into the association network linking PSE-induced alterations in rumen microbiota, microbial metabolites, and host muscle metabolism in relation to goat meat quality. These findings suggest that PSE supplementation may improve meat quality through coordinated changes in rumen microbial ecology and muscle metabolic profiles.},
}

@article {pmid42870454,
year = {2026},
author = {Khafagy, ES and El-Kimary, GI and Al Saqr, A and Hegazy, WAH},
title = {The Oral Virome in Dental Caries: From Ecological Disruptors to Therapeutic Opportunities.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604028},
doi = {10.4014/jmb.2604.04028},
pmid = {42870454},
issn = {1738-8872},
mesh = {*Dental Caries/therapy/virology/microbiology ; Humans ; Biofilms/growth & development ; *Virome ; *Mouth/virology/microbiology ; Bacteriophages/physiology/genetics ; Animals ; Dysbiosis ; Streptococcus mutans/virology ; Microbiota ; },
abstract = {Dental caries results from ecological dysbiosis of oral biofilms driven by frequent sugar exposure, yet the role of viruses, particularly bacteriophages, in this process remains underexplored. This review synthesizes current evidence on how the oral virome contributes to caries pathogenesis and examines emerging phage-based therapeutic strategies. The oral cavity harbors diverse viral communities, including eukaryotic viruses (herpesviruses, papillomaviruses) and prokaryotic viruses (bacteriophages). While herpesviruses like EBV, CMV, and HSV-1 do not directly demineralize teeth, they may act as ecological stressors by modulating host immunity, altering gingival crevicular fluid composition, and promoting inflammation that favors cariogenic bacterial activity. Bacteriophages function as key ecological regulators through "kill-the-winner" dynamics, maintaining microbial diversity by preying on dominant species. However, temperate phages can horizontally transfer genes encoding acidogenicity, biofilm formation, or antibiotic resistance, potentially accelerating dysbiosis. Metagenomic studies reveal distinct salivary phage signatures associated with caries, suggesting diagnostic potential. Preclinical evidence demonstrates that lytic phages targeting Streptococcus mutans (e.g., SMHBZ8, ΦAPCM01) disrupt biofilms in vitro and prevent caries in ex vivo and murine models. Phage-derived enzymes (endolysins, depolymerases) and peptides offer additional precision antimicrobials with minimal commensal disruption. Despite promising advances, significant translational gaps remain, including limited well-characterized phages, insufficient polymicrobial model testing, and absence of human clinical trials. Integrating virome ecology into caries management represents a paradigm shift from pathogencentric approaches toward ecosystem-based therapeutics, with phages offering targeted, self-replicating, and evolutionarily dynamic tools for restoring oral health.},
}

*Dental Caries/therapy/virology/microbiology
Humans
Biofilms/growth & development
*Virome
*Mouth/virology/microbiology
Bacteriophages/physiology/genetics
Animals
Dysbiosis
Streptococcus mutans/virology
Microbiota

@article {pmid42870579,
year = {2026},
author = {Zhu, YH and Li, X and Liu, Z and Liu, J and Ye, R and Xue, W and Jiang, G},
title = {DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag571},
pmid = {42870579},
issn = {1477-4054},
support = {2025AIYJSZX-YB006//Fundamental Research Funds for the Central Universities/ ; BK20230102//Natural Science Foundation of Jiangsu Province/ ; 62402227//National Natural Science Foundation of China/ ; 42677660//National Natural Science Foundation of China/ ; 42477122//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Bayes Theorem ; Clustering Algorithms ; *Metagenome ; Microbiota ; Cluster Analysis ; Algorithms ; Autoencoder ; },
abstract = {Accurate metagenomic binning is essential for reconstructing microbial genomes, thereby facilitating the discovery of novel taxa, the identification of pathogens, and the characterization of antimicrobial resistance genes. Most existing methods are designed for assembled contigs and cannot be directly applied to raw long reads. Although a few dedicated long-read binning methods have emerged, challenges remain in bin-number estimation and representation learning. Here, we propose Deep Embedded Clustering for Long-read Binning (DecBin), an adaptive method for directly binning raw long reads through integrating a variational autoencoder (VAE), Bayesian optimization, and deep embedded clustering within a unified framework. Computational experiments on large-scale simulated and mock-community datasets demonstrate that DecBin outperforms state-of-the-art methods in both long-read binning and metagenome-assembled genome recovery, while also achieving strain-level resolution in a low-complexity natural microbiome. Further analysis shows that the advantage of DecBin is partly attributable to its Davies-Bouldin index-guided Bayesian optimization, which explicitly evaluates candidate cluster numbers using a global cluster-validity criterion, thereby improving bin-number estimation across communities of varying complexity. Meanwhile, joint fine-tuning of the VAE encoder and clustering layer enables clustering feedback to refine the latent space, yielding representations better aligned with genome partitions. These findings highlight the potential of adaptive deep clustering for metagenomic binning directly from raw long reads without prior assembly. The source code of DecBin is freely available at https://github.com/LorMeBioAI/DecBin.},
}

*Metagenomics/methods
Bayes Theorem
Clustering Algorithms
*Metagenome
Microbiota
Cluster Analysis
Algorithms
Autoencoder

@article {pmid42871002,
year = {2026},
author = {Mao, W and Yang, Y and Yu, X and Wu, C and Zhao, W and Huang, N},
title = {Q fever with biliary dilatation following contact with muntjac deer: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1942956},
pmid = {42871002},
issn = {2296-858X},
abstract = {Q fever is a zoonosis caused by Coxiella burnetii. Classic presentations include atypical pneumonia and hepatitis, but bile duct dilation on imaging is rarely described. We report a case of acute Q fever in an urban resident of Chengdu, Sichuan Province, Southwestern China, who presented with cholestatic liver injury and intra- and extrahepatic bile duct dilation, highlighting an unusual manifestation that mimicked biliary tract disease. A 53-year-old man was admitted with persistent high fever (up to 41.8 °C), headache, chills, and right upper quadrant pain. Laboratory tests showed cholestatic hepatitis (AST 132 U/L, ALT 110 U/L, ALP 221 U/L, GGT 231 U/L), with normal total and direct bilirubin. Magnetic resonance cholangiopancreatography (MRCP) revealed mild intra- and extrahepatic bile duct dilation without obstruction. The patient had no livestock contact but had been exposed to wild muntjac deer from informal sources. Empiric doxycycline combined with piperacillin-tazobactam led to rapid defervescence and symptom improvement. The diagnosis of acute Q fever was supported by metagenomic next-generation sequencing (mNGS) of peripheral blood, in the absence of confirmatory seroconversion. In this case, bile duct dilation without jaundice was a notable manifestation of the infection. For febrile patients with unexplained cholestasis and bile duct dilation, especially those with a history of contact with wild animals, Q fever should be considered in the differential diagnosis.},
}

@article {pmid42871004,
year = {2026},
author = {Wang, Z and Shen, X and Du, B and Li, W and Church, P and Avignone-Rossa, C and Yang, K and Guo, B},
title = {Propagation of side-stream partial nitritation-anammox disturbance to mainstream wastewater greenhouse gas emissions.},
journal = {NPJ clean water},
volume = {9},
number = {1},
pages = {75},
pmid = {42871004},
issn = {2059-7037},
abstract = {Side-stream partial nitritation-anammox (PN/A) process is energy efficient for nitrogen removal but highly sensitive to disturbances such as high organic loadings from anaerobic digestion (AD) liquor. How such disturbance affects downstream treatment performance and greenhouse gas (GHG) emissions in full-scale plants remains insufficiently understood. Here, a full-scale Anoxic-Aerobic-AD-PN/A wastewater treatment plant was compared during satisfied and disturbed PN/A operation. Under disturbed operation, the mainstream apparent liquid-phase TN removal rate decreased from 472.4 to 298.2 kg-N/d and estimated N2O and CH4 emissions increased by 69.39 kg-N2O/day and 10.99 kg-CH4/day, respectively. Estimated mainstream GHG emissions rose from 61784.2 to 82768.9 CO2-eq.kg/day. A broader comparison including PN/A N2O estimates and biogas-electricity offset also suggested increased climate burden (58997.2 to 77742.1 CO2-eq kg/day). Metagenomic analysis showed marked reductions in the relative abundance of Ca. Brocadia and Nitrosomonas in PN/A, together with a strong depletion of anammox genes, hdh/hzo. Elevated Nitrosomonas-associated cytochrome P460 and higher abundances of nirK/norBC (assigned to Nitrosomonas and Nitrospira) in the Anoxic and Aerobic tanks were consistent with increased nitrifier-associated N2O-production potential. These findings indicate that disturbance of side-stream PN/A can propagate to the mainstream and increase estimated mainstream GHG emissions, highlighting the need to balance AD intensification with stable PN/A operation.},
}

@article {pmid42871005,
year = {2026},
author = {O'Reilly, CB and Giesbrecht, T and Tyson-Carr, J and Murphy, B and Cagney, K and Lenzi, L and Fallon, N and Roberts, CA},
title = {Not all stress is equal: Examination stress and cortisol reactivity are associated with exploratory species-level variation but not broad restructuring of the gut microbiome.},
journal = {Neurobiology of stress},
volume = {45},
number = {},
pages = {100855},
pmid = {42871005},
issn = {2352-2895},
abstract = {BACKGROUND: Psychological stress has been implicated in gut microbiome variation, but human evidence remains inconsistent and often does not distinguish exposure to stressful contexts from individual differences in physiological stress reactivity. This repeated-measures study examined whether naturalistic examination stress and post-awakening cortisol reactivity were associated with gut microbiome diversity, community composition, and species-level differential abundance.

METHODS: Thirty-nine healthy university students were assessed during examination and non-examination periods. At each assessment, participants completed validated measures of perceived stress, anxiety, affect, self-esteem, sleep, diet, and physical activity; provided salivary cortisol samples at awakening, 30 min, and 45 min post-awakening; and collected a stool sample for whole-metagenome shotgun sequencing. Post-awakening cortisol reactivity was indexed using area under the curve with respect to increase.

RESULTS: Examination stress was associated with increased perceived stress, state and trait anxiety, negative affect, poorer subjective sleep, and amplified post-awakening cortisol reactivity. Alpha and beta diversity of the gut microbiome did not differ between examination and non-examination periods, and within-subject changes in community composition were not associated with changes in cortisol reactivity. However, exploratory species-level analyses identified nominal selective microbial differences. Examination stress was associated with higher relative abundance of Dialister massiliensis and Lawsonibacter asaccharolyticus, alongside lower Duodenibacillus massiliensis and Sutterella wadsworthensis. Cortisol reactivity showed distinct associations with higher Roseburia hominis and Ruminococcus bicirculans, and lower Methanobrevibacter smithii. Within-subject increases in cortisol reactivity also covaried with higher Dabirmavirus hominis, Phascolarctobacterium succinatutens and lower Coprococcus catus.

CONCLUSIONS: Short-term examination stress was associated with marked psychological and endocrine responses but was not accompanied by broad restructuring of the adult gut microbiome. Instead, exploratory findings suggest that examination stress and cortisol reactivity may be reflected in selective species-level microbial variation, supporting further longitudinal and functional investigation of stress-related microbiome dynamics.},
}

@article {pmid42871043,
year = {2026},
author = {Zou, Y and Zhang, W and Gao, A and Fu, J and Sui, Y},
title = {Beyond community state types: vaginal microbial diversity and CST-IV signatures are associated with pregnancy in euploid embryo transfer cycles.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1881146},
pmid = {42871043},
issn = {1664-2392},
mesh = {Female ; Humans ; *Embryo Transfer/methods ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; Pregnancy Outcome ; Adult ; Fertilization in Vitro ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Pregnancy Rate ; },
abstract = {BACKGROUND: Despite significant progress in assisted reproductive technology, in vitro fertilization (IVF) pregnancy rates remain suboptimal. Although the vaginal microbiome has been implicated in IVF outcomes, prior studies often overlooked embryonic aneuploidy, a major confounder. This study aimed to investigate the association between the vaginal microbiome and pregnancy outcomes in euploid embryo transfer cycles.

METHODS: This prospective study included 109 single euploid blastocyst transfer cycles. Upper vaginal swabs were collected on the transfer day and subjected to 16S rRNA gene sequencing. Microbial α- and β-diversity, community state types (CSTs), and differentially abundant taxa were compared between the clinical pregnancy (CP, n = 55) and non-clinical pregnancy (NCP, n = 54) groups.

RESULTS: The NCP group exhibited significantly higher vaginal microbial richness (Chao1, p = 0.029; ACE, p = 0.029) and distinct β-diversity compared with the CP group (R² = 0.049, p = 0.002), whereas CST distribution did not differ between groups. Within the non-Lactobacillus-dominant CST-IV subgroup, the CP group was relatively enriched in Bifidobacteriaceae (LDA = 5.0) with predicted fermentative pathways, whereas the NCP group showed higher relative abundances of Prevotella (LDA = -4.1), Dialister (LDA = -3.6), and Peptoniphilus (LDA = -2.3), accompanied by predicted tryptophan degradation and oxidative stress pathways.

DISCUSSION: These findings, derived mainly from computational prediction, suggest that fine-scale taxonomic and functional composition, rather than broad CST classification, may influence pregnancy outcomes following euploid embryo transfer, offering preliminary insights for microbiome-informed strategies to optimize reproductive outcomes. Future longitudinal studies incorporating shotgun metagenomics and metabolomics in independent cohorts are warranted to validate these preliminary observations and to clarify the dynamic association between vaginal microbiota and IVF pregnancy outcomes.},
}

Female
Humans
*Embryo Transfer/methods
*Vagina/microbiology
Pregnancy
*Microbiota
Pregnancy Outcome
Adult
Fertilization in Vitro
Prospective Studies
RNA, Ribosomal, 16S/genetics
Pregnancy Rate

@article {pmid42871162,
year = {2026},
author = {Zhou, S and Cao, M and Tang, J and Chen, C and Zhang, N and Wu, T and Chen, K},
title = {Contrasting ecological responses of abundant and rare bacterial and fungal subcommunities along an alpine marsh wetland degradation gradient.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1970129},
pmid = {42871162},
issn = {1664-302X},
abstract = {INTRODUCTION: Abundant and rare microbial taxa may respond differently to wetland degradation, yet their relative contributions to community reorganization remain poorly resolved in alpine marsh wetlands.

METHODS: We investigated lightly (LD), moderately (MD), and severely degraded (SD) alpine marsh wetlands on the northern shore of Qinghai Lake using 15 soil metagenomes and nine soil physicochemical properties. Bacterial and fungal genera were classified as abundant, intermediate, rare, or low-prevalence taxa according to domain-specific prevalence and mean relative abundance. Sample-level richness and original abundance contributions, alpha and beta diversity, community composition, distribution breadth, candidate indicator genera, and environmental associations were compared across the degradation gradient.

RESULTS: Total detected bacterial richness declined from 346.2 genera per sample in LD to 287.0 in SD. The rare bacterial share of detected richness decreased from 45.3% to 40.4%, while its original abundance contribution decreased from 6.79% to 3.70%. Abundant fungi accounted for 97.1-98.5% of total fungal abundance. Rare bacterial richness declined monotonically with degradation, whereas Shannon diversity, Simpson diversity, and Pielou's evenness declined in abundant fungi. All four focal subcommunities differed significantly in composition among degradation levels, with the largest PERMANOVA effect observed for abundant fungi and the smallest for rare fungi. Rare fractions exhibited greater incidence-based beta diversity and narrower observed distributions than abundant fractions. Soil PC1 and PC2 were associated with 51.6%, 41.4%, and 55.1% of the variation in abundant bacterial, rare bacterial, and abundant fungal communities, respectively, but with only 0.6% of the variation in rare fungal communities.

DISCUSSION: Partitioning microbial communities into abundant and rare fractions revealed pronounced abundance- and domain-dependent reorganization along the wetland degradation gradient. Rare bacteria showed marked losses in richness and abundance contribution, whereas abundant fungi exhibited stronger declines in within-community diversity and greater environmental structuring. These contrasting responses were obscured in whole-community summaries, highlighting the value of explicitly separating abundant and rare taxa when evaluating microbial responses to alpine marsh wetland degradation.},
}

@article {pmid42871255,
year = {2026},
author = {Yang, S and Zhu, M and Cheng, Z},
title = {Cat scratch disease with fever and lymphadenopathy without definite cat exposure diagnosed via tissue metagenomic next-generation sequencing technology: a case report.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {210},
pmid = {42871255},
issn = {2523-1995},
abstract = {BACKGROUND: Cat scratch disease (CSD), a disease caused by Bartonella henselae (B. henselae), is often associated with exposure to cats. However, in rare cases, a history of cat exposure is absent, and thus achieving a definitive diagnosis may be challenging. Metagenomic next-generation sequencing (mNGS) is a relatively new technology that can analyze pathogens without introducing inherent biases. In this report, we describe a case of CSD diagnosed via mNGS, which supports the use of mNGS in identifying rare types of pathogenic infection.

CASE DESCRIPTION: A 54-year-old male exhibited fever and headache of unknown cause, with a history of working at a chicken farm and no clear cat exposure. Routine antibiotic treatment for infection was ineffective. Lymph node biopsy demonstrated granulomas accompanied by chronic suppurative inflammation and abscess formation. A biopsy sample from the parotid lymph node was subjected to mNGS, which revealed the presence of B. henselae and led to a subsequent diagnosis of CSD. After treatment with azithromycin, the patient recovered and was discharged. At the 3-month telephone follow-up, the patient was asymptomatic.

CONCLUSIONS: CSD in patients with prolonged fever plus culture-negative granulomatous lymphadenopathy or similar compatible findings, even when the exposure history is atypical，and mNGS, as an effective examination method, can aid in arriving at a definitive diagnosis.},
}

@article {pmid42871338,
year = {2026},
author = {Liu, Y and Liu, Y and Huang, S and Zhao, Y and Zhu, L and Wang, T and Liang, H and Liu, M and Geng, W},
title = {Correction: Systemic lupus erythematosus complicated by refractory Mycobacterium avium complex infection involving bilateral lower extremities: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1999626},
doi = {10.3389/fmed.2026.1999626},
pmid = {42871338},
issn = {2296-858X},
abstract = {[This corrects the article DOI: 10.3389/fmed.2026.1936197.].},
}

@article {pmid42871598,
year = {2026},
author = {Manjunatha Reddy, BG and Jabeen, U and Kharva, H and Ramakrishnan, MA},
title = {Environmental surveillance: harnessing environmental sample data to protect animal health.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1965480},
pmid = {42871598},
issn = {2297-1769},
abstract = {Infectious diseases in domestic animals-including those with zoonotic potential-impose a substantial global burden on food security, livelihoods, and public health. Environmental surveillance (ES) offers a critical complement to conventional animal-level diagnostics by detecting pathogens or their genetic signatures directly in the matrices through which they persist and spread: water, soil, air, manure, fomites, and arthropod vectors. This review synthesizes evidence across three analytical dimensions-matrix suitability, detection method performance, and wastewater-based epidemiology (WBE)-for 15 viral, bacterial, and parasitological diseases of domestic animals. Key findings reveal that matrix choice profoundly governs detection sensitivity: surface water and wetland sediments support infectious avian influenza virus isolation; pooled environmental feces and slurry outperform individual animal sampling for Mycobacterium avium subsp. paratuberculosis (MAP); and electrostatic dust cloths enable simultaneous detection of peste-des-petits ruminants virus (PPRV) and capripoxviruses at livestock markets. Molecular methods, principally quantitative RT-PCR and droplet digital PCR, consistently outperform conventional culture in sensitivity and turnaround time, though viability-linked assays remain an important unresolved need. WBE is increasingly applied beyond human pathogens: piggery effluent surveillance for Japanese encephalitis virus and wastewater metagenomics for antimicrobial resistance exemplify its veterinary potential. Interpretive limitations persist, including matrix-driven inhibition, absence of harmonized protocols, and the challenge of equating nucleic-acid signals with infectious risk. Realizing the full promise of ES within a One Health framework requires standardized, field-validated sampling workflows, viability-linked molecular assays, and formal integration of environmental signals into routine veterinary surveillance and outbreak-response systems.},
}

@article {pmid42872065,
year = {2026},
author = {Alberdi, A and Aizpurua, O},
title = {From humans to the wild: revisiting assumptions in gut microbiome analysis.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag168},
pmid = {42872065},
issn = {2730-6151},
}

@article {pmid42872861,
year = {2026},
author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ},
title = {Environmental gradients shape the hydrocarbon-degrading microbiome in two mid-Atlantic bays.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0086626},
doi = {10.1128/msystems.00866-26},
pmid = {42872861},
issn = {2379-5077},
abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that is released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome-assembled genomes (MAGs) from these estuaries. In the surface waters of both estuaries, aerobic aromatic and alkane degradation pathways predominated, with higher gene abundances observed in low-salinity spring and summer samples. Salinity significantly structured both hydrocarbon-degrading MAG abundances, alongside temperature, nitrate, and silicate concentrations, and hydrocarbon degradation gene expression, which additionally varied seasonally, with the highest relative expression of aromatic degradation genes in low-salinity samples. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition-dependent metabolic coupling, while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. Together, these results support our hypothesis that environmental gradients and taxon-specific metabolic strategies jointly structure the abundance and in situ activity of hydrocarbon degraders, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.

IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems, yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.},
}

@article {pmid42872902,
year = {2026},
author = {Shu, S and Shen, Y and Wuri, L and Jia, Y and Li, A and Ding, J and Wang, H},
title = {Field-validated microbial deodorant reduces hazardous gas exposure and improves air quality in rural household toilets.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {53},
number = {},
pages = {},
doi = {10.1093/jimb/kuag024},
pmid = {42872902},
issn = {1476-5535},
support = {QD202419//MARA/ ; No. 2024YFD1600201//National Key Research and Development Program of China/ ; },
mesh = {Hydrogen Sulfide/metabolism/analysis ; Ammonia/metabolism/analysis ; *Bacteria/metabolism/genetics/isolation & purification/classification ; *Toilet Facilities ; Sewage/microbiology ; *Odorants/prevention & control/analysis ; Air Pollutants/metabolism/analysis ; *Air Pollution, Indoor/prevention & control/analysis ; },
abstract = {Malodorous emissions from rural sanitation systems pose a direct environmental health concern. This study developed a composite microbial deodorant (CMD) using five bacterial strains isolated from activated sludge, combined in an optimal 1:1:1:1:1 ratio determined by orthogonal testing, to mitigate emissions of NH3 and H2S-key hazardous and odorous pollutants. In laboratory simulations, the CMD reduced NH3 and H2S by 82.1% and 86.1%, respectively. A pivotal 6-month field evaluation in three common types of rural household toilets demonstrated sustained, real-world efficacy, with peak removal rates of 79.43% for NH3 and 80.83% for H2S. The intervention also conserved nitrogen, reducing total nitrogen loss by 14.8%. Metagenomic analysis revealed the mechanistic basis: the CMD reshaped microbial metabolic pathways by upregulating genes for nitrification (hao) and sulfur oxidation (sqr), while suppressing reductive genes (nif, aprA), thus curbing emissions at source. This work provides robust field evidence that an in situ microbial strategy can effectively and sustainably improve household air quality in rural settings, offering a practical, low-cost, and eco-friendly solution for in situ odor control in rural sanitation- a critical step for sustaining the health benefits of the ''Toilet Revolution'' and improving rural living environments. One-Sentence Summary A composite microbial deodorant effectively reduces ammonia and hydrogen sulfide emissions and improves air quality in rural household toilets through 6-month field validation, providing an eco-friendly and low-cost odor control solution for rural sanitation.},
}

Hydrogen Sulfide/metabolism/analysis
Ammonia/metabolism/analysis
*Bacteria/metabolism/genetics/isolation & purification/classification
*Toilet Facilities
Sewage/microbiology
*Odorants/prevention & control/analysis
Air Pollutants/metabolism/analysis
*Air Pollution, Indoor/prevention & control/analysis

@article {pmid42873652,
year = {2026},
author = {Pulvino, AT and Sardaro, MLS and Quinn, WG and Christopher, ER and Koenig, S and Lucore, JM and Vidal-Cruchez, O and Mallott, EK and Kuthyar, S and Lee, W and Chitta, S and Gray, S and Williams, LE and Curley, JP and Liechty, ER and Ben-Sahra, I and Amato, KR},
title = {Bile, sulphur and carbohydrate metabolic variation co-occur with host adiposity in mice colonized with primate microbiota.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001848},
pmid = {42873652},
issn = {2057-5858},
mesh = {Animals ; Mice ; Humans ; *Adiposity ; *Bile/metabolism ; Macaca mulatta ; *Sulfur/metabolism ; *Carbohydrate Metabolism ; Multiomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Cecum/microbiology ; Liver/metabolism ; Metagenomics ; Primates/microbiology ; Microbiota ; },
abstract = {Although mechanistic links between the microbiome and chronic disease are increasingly well defined, how microbiomes facilitate normal variation in host metabolism remains less clear. Building on our recent demonstration that pooled faecal inocula from different primate species can cause relative differences in mouse host adiposity, we define potential mechanisms by which this could occur. Using existing samples from germ-free mice inoculated with faecal samples from humans (Homo sapiens), rhesus macaques (Macaca mulatta) and squirrel monkeys (Saimiri boliviensis), we integrate shotgun metagenomics of caecal contents, liquid chromatography-MS-MS metabolomics of serum and caecal contents and hepatic RNA-sequencing. Our multi-omic analysis reveals that the relative increase in adiposity previously observed in macaque-donor mice is associated with differences in hepatic cysteine catabolism and bile metabolism pathway features. These data suggest that bile and sulphur co-metabolic variation may mediate increased bile pool hydrophobicity. We also observed variation in caecal microbiome composition as well as host hepatic retinol signalling and lipid metabolism between treatments. When considered together with the observation that macaque-donor mice consumed less food than the other treatment groups, our results support the hypothesis that increased bile pool hydrophobicity results in increased dietary energy extraction. Our findings provide a foundation for future mechanistic testing of new hypotheses for understanding how the intestinal microbiomes of different primate species regulate lipid homeostasis in a mouse host.},
}

Animals
Mice
Humans
*Adiposity
*Bile/metabolism
Macaca mulatta
*Sulfur/metabolism
*Carbohydrate Metabolism
Multiomics
Feces/microbiology
*Gastrointestinal Microbiome
Cecum/microbiology
Liver/metabolism
Metagenomics
Primates/microbiology
Microbiota

@article {pmid42874194,
year = {2026},
author = {Luo, ZN and Zhang, TY and Zhu, B and Zhang, DX and Lv, H and Shi, J and Peng, Z and Zhou, B and Xu, M and Zhao, HX and He, H and Zeng, C and Xu, B},
title = {Nitrification control and early microbiome-resistome transitions during permanent conversion from chloramine to free chlorine in a full-scale drinking water distribution system.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127125},
doi = {10.1016/j.watres.2026.127125},
pmid = {42874194},
issn = {1879-2448},
abstract = {Chloramine is widely used in drinking water distribution systems (DWDSs), but ammonia recycling can promote nitrification and disinfectant residual loss. As source water ammonia is controlled, permanent conversion to free chlorine may replace repeated temporary chlorine burns, yet its nitrogen control performance and microbiome-resistome consequences remain unresolved. We analyzed early responses of 16 bulk water metagenomes from four sites at chloramine baseline and free chlorine days 1, 5 and 8, with nitrification-related water quality monitored for 8 months. Conversion achieved nitrogen control benefits, with nitrite lower after conversion at multiple time points (p < 0.05), dominant nitrifying genera suppressed to <0.1%, and ammonia oxidation and hydroxylamine oxidation potentials decreasing from 125.84 to 2.77 TPM and from 20.35 to 0.45 TPM. Community restructuring was site-specific (PERMANOVA stage R[2] = 0.297, p = 0.001; site R[2] = 0.311, p = 0.002). Despite improved nitrification control, 21-50% of each site's baseline ARGs remained detectable after conversion. SEM linked chlorine speciation to community shift (β = 0.695) and ARG/16S shift (β = -0.344), while community shift and MGE/16S shift showed positive paths to ARG/16S shift (β = 0.426 and 0.819). The pathways suggest that the shift toward free chlorine was a potential driver of early microbiome-resistome reorganization. These early responses are consistent with succession from chloramine-resistant communities toward free chlorine-resistant, MGE-associated hosts that may facilitate ARG redistribution. Permanent conversion is a viable nitrification control option, but evaluation should include microbiome and resistome monitoring beyond residual and nitrification indicators.},
}

@article {pmid42874200,
year = {2026},
author = {Zhang, H and Yan, R and Wang, J and Fang, L and Huang, X and Wen, T and Zhang, Y and Yu, L and Yang, K and Zhang, Y and Tang, Z and Lakshmanan, P and Zhang, J and Wang, B and Qiu, Y and Chen, X and Shi, X and Su, X},
title = {Viral regulation of N2O emissions depends on soil acidity.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143897},
doi = {10.1016/j.jhazmat.2026.143897},
pmid = {42874200},
issn = {1873-3336},
abstract = {Acidification generally enhances N2O emissions from soils. Yet, the adaptive responses of denitrifiers and the regulatory roles of soil viruses in denitrifier-mediated N2O emissions under persistent acidity remain poorly understood. Here, we combined D2O-labeled single-cell Raman spectroscopy, [15]N tracing, metagenomics, machine learning, and virus-addition experiments to examine virus-denitrifier interactions across soils with contrasting long-term acidity conditions maintained for > 17 years. Acidic soils showed the highest N2O emissions despite the lowest potential denitrification rate and highest microbial anabolic activity. Denitrifiers and viral populations in acidic soils exhibited reduced microdiversity, stronger purifying selection, and distinct functional specialization, while viruses showed a lower virulent-to-temperate ratio and greater genetic potential for host interaction and persistence. Host antiviral defense capacity was the strongest genomic predictor of abundance responses to active virus. In acidic soils, active viruses increased N2O reductase level by 33.2% without altering nosZ abundance and reduced N2O accumulation by up to 62.5%, indicating an efficiency-optimized response. Neutral soils showed a quantity-driven response, whereas alkaline soils showed no significant reduction in N2O accumulation. These findings reveal acidity-dependent viral regulation of N2O emissions, strongest in long-term acidic soils.},
}

@article {pmid42874205,
year = {2026},
author = {Fang, K and Chu, S and Lu, Z and Ma, X and Zhang, D and Ding, W and Wei, L and Yang, H and Zhou, R and Zhang, D and Zhou, P},
title = {Sustained hydrogen delivery enhances microbiome-associated cadmium and copper immobilization in co-contaminated soils.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143893},
doi = {10.1016/j.jhazmat.2026.143893},
pmid = {42874205},
issn = {1873-3336},
abstract = {Molecular hydrogen (H2) is an important energy source for soil microbes and has been implicated in biogeochemical regulation; however, whether-and how-exogenous H2 inputs promote Cd and Cu immobilization in co-contaminated soils remains unclear. We engineered MgH2-biochar granules capable of sustained H2 release for up to 448 h. The granules exhibited high adsorption capacities in aqueous Cd-Cu systems (Cu: 59.76 mg g[-1]; Cd: 35.76 mg g[-1]). In soil, MgH2-biochar treatment was associated with enhanced microbial hydrogenase activity, reduced oxidative stress, and enrichment of functional taxa, together with significant reductions in available Cd (10.9-22.5%) and Cu (14.2-30.1%) (P < 0.05). Notably, Mg-associated alkalization elevated soil pH and contributed to physicochemical immobilization. Microbial community analyses further revealed H2-associated shifts in community structure and significant associations between H2 metabolism and metal resistance (Cd: P < 0.001; Cu: P < 0.03). Genome-resolved metagenomics identified 10 metagenome-assembled genomes (MAGs) that co-harbour [NiFe]-hydrogenases (Groups 1 and 4) and Cd/Cu resistance genes (e.g., actS, czcA, and copC). Exploratory pathway modeling further indicated associations of Cd/Cu immobilization with H2-associated microbial processes and Mg-associated physicochemical effects. This work provides integrated material, geochemical, and microbial evidence supporting an H2-associated contribution to heavy-metal immobilization in soils.},
}

@article {pmid42862088,
year = {2026},
author = {Hoque, MN and Rahman, MS and Hossain, MG and Rahman, MT and Islam, T and Hossain, MA},
title = {Subclinical Mastitis and Antibiotic Exposure Reshape the Milk Bacteriome, Resistome, and Metabolic Functional Profiles in Dairy Cows.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70440},
pmid = {42862088},
issn = {2045-8827},
support = {LS20221764//Bangladesh Bureau of Educational Information & Statistics (BANBEIS), Ministry of Education/ ; },
mesh = {Animals ; *Milk/microbiology ; Female ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Cattle ; *Bacteria/drug effects/classification/genetics/isolation & purification ; *Mastitis, Bovine/microbiology/drug therapy ; Metagenomics ; *Microbiota/drug effects ; Drug Resistance, Bacterial ; },
abstract = {Subclinical mastitis (SCM) reduces milk yield and promotes antibiotic use, contributing to antimicrobial resistance. However, information on milk microbiome dysbiosis and resistome alterations in dairy cows remains limited. We performed shotgun metagenomic sequencing of 30 milk samples from 20 cows classified as SCM (n = 10), antibiotic-treated (ANT; n = 10), and healthy milk (HM; n = 10). Bacteriome, resistome, and metabolic functions were analyzed using bioinformatic tools. Microbial alpha diversity was significantly higher in HM than SCM and ANT samples (p < 0.05), with the greatest richness observed in Local Zebu and Middle-aged (5-8 years) cows. However, beta diversity did not differ significantly among groups (PERMANOVA, p > 0.05). A total of 665 bacterial species belonging to 15 phyla were identified, with Pseudomonadota, Actinomycetota, and Bacillota comprising 90%-99% of total abundance. SCM milk was dominated by Actinoalloteichus sp. (40.55%) and Vibrio furnissii (37.01%), while Staphylococcus aureus was enriched (1.74%) compared with HM and ANT (< 0.01%). ANT milk showed increased abundance of Acinetobacter johnsonii (10.52%), whereas HM samples contained beneficial commensals, including Pseudomonas lundensis, Bacteroides thetaiotaomicron, and Lactococcus lactis. Similar taxonomic shifts were observed across breeds and age groups. In total, 194 antimicrobial resistance genes (ARGs) were detected, with SCM harboring the largest repertoire (n = 161). Nevertheless, macrolide-, aminoglycoside-, and β-lactam-resistance genes were significantly enriched in ANT samples (p < 0.01). Correlation analyses linked Escherichia coli and A. johnsonii with multiple ARGs, while Acinetobacter and Pseudomonas were associated with lipid metabolism, membrane transport, and xenobiotic biodegradation pathways. These findings reveal bacteriome disruption, ARG enrichment, and functional alterations in SCM and antibiotic-exposed milk.},
}

Animals
*Milk/microbiology
Female
*Anti-Bacterial Agents/pharmacology/therapeutic use
Cattle
*Bacteria/drug effects/classification/genetics/isolation & purification
*Mastitis, Bovine/microbiology/drug therapy
Metagenomics
*Microbiota/drug effects
Drug Resistance, Bacterial

@article {pmid42862294,
year = {2026},
author = {Yin, Z and Yang, Z and Sun, C and Liu, Z},
title = {Community succession and functional trait reorganization in a continuous aerobic denitrification reactor under repeated hydraulic retention time reductions.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {42862294},
issn = {1615-7605},
support = {National Natural Science Foundation//National Natural Science Foundation of China/ ; },
abstract = {Aerobic denitrification enables nitrogen removal under oxygen-rich conditions, yet its microbial response to hydraulic retention time (HRT) disturbance remains unclear. Here, a continuous aerobic denitrification reactor inoculated with activated sludge enriched in aerobic denitrifiers was operated by stepwise shortening of HRT from 108 h to 60 h. 16S rRNA gene amplicon sequencing and metagenomic sequencing were used to characterize microbial succession, functional adaptation, and co-occurrence network reorganization. Nitrogen removal efficiency remained above 80% under a high influent nitrogen load of 300 mg N/L, comprising about 150 mg/L NH4[[+]]-N and 150 mg/L NO3[[-]]-N, despite marked taxonomic turnover. The alpha diversity of the microbial community decreased from 3.01 ± 0.13 to 2.24 ± 0.38, whereas metagenomic gene diversity remained relatively stable at approximately 13.30 ± 0.12, showing that gene-level diversity did not decline in parallel with microbial diversity. Dominant aerobic denitrifiers shifted from Aquimonas to Pseudofulvimonas. Network analysis showed that Aquimonas contributed more to within-module connectivity, whereas Pseudofulvimonas exhibited stronger among-module connectivity under short HRT. Short HRT enriched genes related to biofilm formation, adhesion, fimbriae, membrane proteins, and pilus assembly. These results indicate that community succession, functional trait reorganization, and redistribution of network roles accompanied stable aerobic denitrification under hydraulic disturbance.},
}

@article {pmid42863152,
year = {2026},
author = {Han, H and Zhou, L and Yu, M and Wang, S and Sha, H and Peng, X},
title = {Systematic insights into 6PPD-quinone biotransformation by acclimated aerobic sludge: Kinetics, pathways, toxicity, and enzymatic mechanisms.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143870},
doi = {10.1016/j.jhazmat.2026.143870},
pmid = {42863152},
issn = {1873-3336},
abstract = {This study acclimated aerobic (AeS), nitrifying (NS), and denitrifying (DS) sludge systems to N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) at 1-20 mg·L[-1] . Within an environmental to high concentration range (1 μg·L[-1] to 5 mg·L[-1]), acclimated AeS removed 88.9%-95.2% of 6PPD‑Q within 14 days, significantly outperforming the NS and DS systems. The first-order degradation rate constant of the aerobic sludge ranged from 0.175 to 1.006 d[-1] . Based on the Haldane kinetic model, its substrate inhibition constant was 29.3 mg·L[-1] , demonstrating the broadest substrate tolerance range. This study proposed 13 biotransformation products (7 of which were reported for the first time), and constructed a complete degradation pathway accordingly. Ecological Structure-Activity Relationship modeling and in vitro bioassays jointly confirmed that AeS treatment significantly reduced the acute toxicity of 6PPD-Q. Metagenomic binning identified Sphingopyxis, Achromobacter, and Pseudomonas as the dominant genera, while molecular docking further implicated cytochrome P450 and peroxidase may serve as key enzymes in the catabolism of the parent compound. A 40‑day experiment showed that combining acclimated aerobic sludge with activated sludge significantly reduced 6PPD‑Q concentrations in real wastewater effluents. This study systematically elucidated the degradation pathway, toxicity evolution, and enzymatic mechanisms of 6PPD-Q in activated sludge, providing new insights for its bioremediation.},
}

@article {pmid42863410,
year = {2026},
author = {Villa-Rodríguez, E and Ferguson, S and Stougaard, J and Radutoiu, S},
title = {Understanding genetic determinants of bacterial adaptation to plant niches: Toward more robust bioinoculant design.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128760},
doi = {10.1016/j.micres.2026.128760},
pmid = {42863410},
issn = {1618-0623},
abstract = {Plant-associated bacteria offer a sustainable alternative to chemical inputs in agriculture, yet the field performance of microbial inoculants remains inconsistent. A central but frequently overlooked cause is that bioprospecting pipelines still select strains on the basis of plant-growth-promoting activities, while the bacterial genetic traits that determine whether a strain can reach, colonise and persist in a given root compartment are rarely assessed. Previous reviews have largely catalogued growth-promoting functions or described root microbiome assembly from the plant's perspective, here we take the bacterium's. We trace the journey of a bacterium from bulk soil to its final niche and, at each stage, identify the genes and pathways (genetic determinants) that encode key bacterial traits involved, such as chemotaxis and motility, nutrient acquisition and metabolic independence, competitive and defensive arsenals, attachment and biofilm formation, evasion of plant immunity, and endophytic entry and persistence. Throughout, we use evidence from comparative genomics and metagenomics, (meta)transcriptomics, targeted mutagenesis and genome-wide screens such as Tn-seq, obtained in systems ranging from binary interactions to synthetic communities and natural soils. For each stage we examine the current state of knowledge, identify critical gaps, and propose avenues to deepen our mechanistic understanding of the bacterial traits involved in plant colonisation. We argue that this mechanistic understanding is the missing foundation for developing inoculants with more consistent and robust performance across diverse agroecosystems.},
}

@article {pmid42863635,
year = {2026},
author = {Xu, R and Wang, Z and Shi, L and Guo, J and Che, B and Li, X and Zhao, X and Sun, D and Zhang, B and Wang, Y and Peng, W},
title = {Metagenomic and systematic analyses reveal the association between hemoglobin levels and metabolic disorders: an open cohort study of Tibetan adults in Qinghai Plateau.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113608},
doi = {10.1016/j.diabres.2026.113608},
pmid = {42863635},
issn = {1872-8227},
abstract = {AIM: Hemoglobin (Hb) varies with altitude, but evidence linking Hb levels to metabolic diseases in high-altitude populations remains limited. We examined associations between Hb and seven metabolic diseases in high-altitude adults and potential mediation by gut microbiota.

METHODS: We analyzed an observational cohort of 1,646 Tibetan adults from the Qinghai Plateau, stratified by Hb tertiles. Mixed-effects logistic regression and generalized additive mixed models assessed Hb-metabolic disease associations using pooled person-time data. Gut metagenomic sequencing and mediation analysis were performed on 534 fecal samples, with KEGG annotation characterizing microbial functional potential.

RESULTS: Hb correlated positively with six metabolic diseases (P < 0.05). Compared with the lowest tertile (122-151 g/L), the highest Hb tertile (169-252 g/L) showed significantly increased adjusted ORs for diabetes (10.02; 95% CI 3.00-33.43), hypertension (2.08; 1.14-3.80), hypercholesterolemia (3.04; 1.24-7.45), hypertriglyceridemia (4.66; 1.60-13.56), overweight/obesity (5.15; 1.83-14.48) and metabolic syndrome (4.58; 2.50-8.38). High Hb were associated with differences in gut microbiota β-diversity (P = 0.001) and composition. Prevotella and Collinsella were enriched in high-Hb, Bifidobacterium and Anaerostipes dominated low-Hb. Twenty-three microbial species mediated Hb-metabolic relationships. Fructose-mannose metabolism and oxidative phosphorylation were enriched in high-Hb, while ABC transporters and fatty acid biosynthesis/metabolism were upregulated in low-Hb.

CONCLUSION: Hb may serve as a useful biomarker for metabolic risk assessment in high-altitude populations, with gut microbiota potentially mediating this association.},
}

@article {pmid42863714,
year = {2026},
author = {Zheng, H and Ma, H and Ran, X and Chai, H},
title = {Mixed carbon source strategy sustains long-term nutrient removal in pyrite-based bioretention systems: Insights into potential nitrogen-sulfur coordination.},
journal = {Bioresource technology},
volume = {464},
number = {Pt C},
pages = {136059},
doi = {10.1016/j.biortech.2026.136059},
pmid = {42863714},
issn = {1873-2976},
abstract = {Bioretention systems (BSs) are widely used for urban stormwater management, yet sustaining nutrient removal over long-term operation remains challenging. A 483-day experiment evaluated a 1:1 woodchip-corncob mixed-carbon formulation in pyrite-based BSs by comparing a mixed carbon source-pyrite system (WCP) with woodchip-pyrite, corncob-pyrite, and pyrite-only systems. Under the tested conditions, the WCP system showed higher observed nutrient removal and a smaller long-term performance decline than the comparison systems, maintaining total dissolved nitrogen and total dissolved phosphorus removal efficiencies of 81.4 ± 3.7% and 73.3 ± 5.8%, respectively, during the long-term stage. Pore-water and fluorescence analyses indicated differences in dissolved organic matter release intensity and composition associated with the mixed-carbon configuration, consistent with more balanced organic electron-donor availability during alternating rainfall and drought periods. 16S rRNA gene sequencing revealed differences in microbial community composition and functional-group distribution, while absolute quantitative metagenomics revealed differences in nitrogen- and sulfur-related functional gene profiles among the composite samples. At the long-term endpoint, the observed electron transport system activity in the WCP system was 21.3%-239.0% higher than the values observed in the comparison systems. The metagenomic profiles and sulfur-related functional patterns were consistent with nitrous oxide-reduction potential and potential coordination between nitrogen and sulfur transformations. Overall, the tested mixed-carbon configuration sustained long-term nutrient removal and was associated with more balanced organic electron-donor availability and potential coordination between nitrogen and sulfur transformations, highlighting its potential for long-term stormwater bioretention.},
}