@article {pmid42098851,
year = {2026},
author = {Dong, J and Cao, Y and Chen, X and Xie, T and Zhang, X and Zhao, Q and Shi, C and Miao, Q and Xu, Z and Yan, L and Dong, L},
title = {Buyang Huanwu Decoction promotes neurorepair after spinal cord injury through a Lactobacillus johnsonii-indole-3-lactic acid-AhR-PI3K/Akt axis.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42098851},
issn = {1749-8546},
support = {YSJ2025009//Postgraduate Research & Practice Innovation Program of Yan'an University/ ; 22XYJ0002//Xi'an Innovation Capability Strong Foundation Plan - Medical Research Project/ ; 2025PT-01//Platform Construction Project of Shaanxi Province's Health and Wellness Scientific Research and Innovation Capacity Enhancement Program/ ; },
abstract = {BACKGROUND: Spinal cord injury (SCI) induces gut microbiota dysbiosis, which significantly affects recovery. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine formula, has shown therapeutic effects on SCI. Although BHD is known to modulate gut microbiota, whether its benefits are mediated through the gut-spinal cord axis remains unclear.

METHODS: A rat SCI model was established. BHD was administered orally, and fecal microbiota transplantation (FMT) from BHD-treated rats (BHD-FMT) was performed to assess neuroprotective and gut-protective effects. Behavioral testing, histology, and immunofluorescence evaluated motor recovery, inflammation, and neuroregeneration. Gut microbiota profiling was performed using 16S rDNA sequencing and metagenomics, while targeted metabolomics quantified tryptophan metabolites. Transcriptomics validated key pathways, and a microbiota-metabolite-signaling network was constructed.

RESULTS: BHD significantly improved motor function, reduced spinal inflammation, and promoted neuronal survival and axonal regeneration. It restored gut function, reduced colonic inflammation, and enhanced ZO-1 and Occludin expression, which were further confirmed by FMT. BHD-FMT reshaped the gut microbiota and enriched Lactobacillus johnsonii, which correlated positively with recovery. Metabolomics showed increased tryptophan metabolites, including indole-3-lactic acid (ILA) and indole-3-propionic acid (IPA), with ILA strongly associated with functional improvement. Transcriptomic analysis and Western blot validation demonstrated that BHD-FMT activated the AhR-PI3K/Akt pathway, which was suppressed by an AhR antagonist.

CONCLUSION: BHD promotes neuroregeneration after SCI by reshaping gut microbiota and enhancing tryptophan metabolism, potentially exerting its effects through the L. johnsonii-ILA-AhR-PI3K/Akt network. These findings reveal a gut-spinal cord axis-mediated mechanism of BHD and highlight microecological targets for SCI therapy.},
}

@article {pmid42098871,
year = {2026},
author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI},
title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02421-w},
pmid = {42098871},
issn = {2049-2618},
support = {BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; },
abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.

RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p < 0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~ 1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~ 2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.

CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.},
}

@article {pmid42098876,
year = {2026},
author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B},
title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02406-9},
pmid = {42098876},
issn = {2049-2618},
support = {2023YFD2000703//National Key R&D Program of China/ ; 2023YFD2000701//National Key R&D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.

RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150 kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20 g/kg dry matter) decreased daily CH4 emissions by ~ 8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.

CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.},
}

@article {pmid42099457,
year = {2026},
author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y},
title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70123},
pmid = {42099457},
issn = {2770-596X},
abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.},
}

@article {pmid42099461,
year = {2026},
author = {Wu, R and Wen, T and Shang, N and Xie, P and Wang, Z and Li, H and Li, S and Zhang, D},
title = {Chondroitin sulfate restores muscle mass via gut-muscle axis remodeling through sugar-bile acid metabolism reprogramming.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70118},
pmid = {42099461},
issn = {2770-596X},
abstract = {Glucocorticoid-induced myopathy is characterized by progressive muscle atrophy and impaired regeneration, yet effective microbiota-oriented interventions for preserving muscle homeostasis remain largely unexplored. Here, we demonstrate that dietary chondroitin sulfate (DCS) restores muscle mass and function through a microbiota-dependent gut-muscle metabolic axis. DCS failed to confer protection in germ-free or antibiotic-treated mice, establishing gut microbiota as a prerequisite for its efficacy. Microbiota transplantation and mono-colonization experiments identified Lactobacillus johnsonii Z-RW as a functionally relevant mediator capable of recapitulating muscle protection under controlled microbial conditions. Integrated metagenomic, metabolomic, and proteomic analyses revealed coordinated reprogramming of intestinal sugar utilization and bile acid metabolism following DCS administration. Notably, DCS promoted bile acid deconjugation and enrichment of secondary bile acids, coinciding with restoration of muscle regenerative and energetic programs, including upregulation of NMRK2, PAX7, and SIRT1. Metabolite supplementation further implicated bile acids as candidate mediators linking microbial metabolism to muscle phenotypes. To quantitatively integrate these shifts, we introduce the sugar-bile acid ratio as a systems-level descriptor of microbiota-driven metabolic remodeling. Our findings delineate a microbiota-dependent metabolic framework through which a functional polysaccharide reshapes intestinal biochemistry to influence distal muscle physiology. This work highlights bile acid-associated signaling as a central relay within the gut-muscle axis and provides a conceptual foundation for microbiota-targeted strategies to mitigate muscle wasting.},
}

@article {pmid42099660,
year = {2026},
author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF},
title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.},
journal = {BJUI compass},
volume = {7},
number = {5},
pages = {e70186},
pmid = {42099660},
issn = {2688-4526},
abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.

SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12 weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.

RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p = 0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p = 0.001), Bray-Curtis (p = 0.008), and nonweighted UniFrac metrics (p = 0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p = 0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p = 0.043) but not of treatment response.

CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.},
}

@article {pmid42100218,
year = {2026},
author = {Hussain, N and Muccee, F and Mirza, AF and Ashraf, NM and Al Haddad, AHI},
title = {Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1778532},
pmid = {42100218},
issn = {2297-1769},
abstract = {Dietary manipulations using probiotics may contribute to the sustainable development of aquaculture. For probiotic applications, their traits, safety profiles, and functional characteristics should be explored. Whole genome sequencing (WGS) can be an informative tool in this regard. We initiated this study to obtain genomic insights into S. solea gut-associated bacteria. Bacteria (n = 20) exhibiting probiotic characteristics were subjected to DNA extraction. A mixture comprising equimolar concentrations of each bacterial DNA was prepared and analyzed through WGS. BV-BRC, metaSPAdes, MetaBAT2, DAS Tool, and PATRIC were used for taxonomic profiling, metagenome assembly, genome binning, comprehensive genome annotation, and subsystem analysis, respectively. For tree construction, MUSCLE and RaxML were employed. Fourteen bins comprising Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota were generated. Among these, the bin comprising the genome of Enterococcus faecium was selected. Its genome comprises 129 contigs with 2,944 coding sequences (CDSs). Genes associated with metabolism, protein processing, stress response, defense and virulence, cellular processes, and cell envelope were identified. Pathways identified included fatty acid and ketone body biosynthesis, glycerolipid and glycerophospholipid metabolism, linoleic acid metabolism, and self-defense mechanisms. This study confirmed the probiotic efficiencies of E. faecium. Hence, this bacterium might be employed as a fish feed supplement in aquaculture.},
}

@article {pmid42100351,
year = {2026},
author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z},
title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100600},
pmid = {42100351},
issn = {2666-5174},
abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.},
}

@article {pmid42100652,
year = {2026},
author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C},
title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799729},
pmid = {42100652},
issn = {2235-2988},
mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; },
abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.},
}

Animals
*Probiotics/administration & dosage
Rats, Wistar
Male
Metagenomics
Rats
Feces/microbiology/chemistry
Disease Models, Animal
*Gastrointestinal Microbiome
*Liver Failure
Cytokines
Ammonia/blood
Dysbiosis
Galactosamine

@article {pmid42100656,
year = {2026},
author = {Li, T and Liu, J and Wang, X},
title = {Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1812778},
pmid = {42100656},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology/immunology ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Molecular Diagnostic Techniques/methods ; },
abstract = {BACKGROUND: Pulmonary infections represent a significant global health concern, contributing substantially to morbidity and mortality worldwide. Metagenomic next-generation sequencing (mNGS) represents an advanced, comprehensive, and unbiased diagnostic approach for pathogen identification, effectively overcoming many limitations inherent in conventional diagnostic methods. This study aimed to systematically evaluate the clinical performance of mNGS in the etiological diagnosis of pulmonary infections, with a particular emphasis on its utility across diverse immune statuses.

METHODS: This retrospective study included 136 patients with suspected pulmonary infections admitted to the Department of Respiratory Medicine at Shandong Provincial Hospital from June 2023 to April 2025. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and concurrently subjected to mNGS and conventional microbiological testing (CMT). The pathogen detection spectrum and diagnostic performance of mNGS were systematically compared against those of CMT.

RESULTS: mNGS exhibited a significantly higher overall pathogen detection rate compared to CMT (77.2% vs. 50.0%, P < 0.001). Regarding the pathogen spectrum, mNGS identified a broader array of microorganisms, encompassing 19 bacterial, 9 fungal, and 2 mycobacterial species, in contrast to the 11 bacterial, 5 fungal, and 1 mycobacterial species detected by CMT. Diagnostic performance analysis further revealed that mNGS sensitivity was significantly superior to that of CMT (74.6% vs. 46.7%, P < 0.001). Furthermore, mNGS demonstrated a distinct advantage in detecting mixed infections, with a detection rate of 19.1%, significantly exceeding that of CMT (8.8%, P < 0.05). Subgroup analysis indicated a significantly higher incidence of mixed infections in immunocompromised patients compared to immunocompetent patients (35.1% vs. 13.1%, P < 0.05). Additionally, immunocompromised patients were more frequently subjected to adjustments in antimicrobial therapy guided by mNGS results (56.8% vs. 35.4%, χ² = 5.094, P < 0.05).

CONCLUSIONS: In conclusion, mNGS offers superior sensitivity and broader pathogen coverage for the etiological diagnosis of pulmonary infections compared to conventional microbiological testing. Its enhanced capability to detect mixed infections significantly improves diagnostic accuracy in immunocompromised patients and effectively facilitates the dynamic optimization of antimicrobial therapy. Serving as a powerful complement to traditional diagnostic methods, mNGS holds particular value for the rapid diagnosis of complex and immunosuppression-associated pulmonary infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Male
Female
*Metagenomics/methods
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
Adult
*Respiratory Tract Infections/diagnosis/microbiology/immunology
Sensitivity and Specificity
Bacteria/genetics/isolation & purification/classification
Fungi/genetics/isolation & purification/classification
Aged, 80 and over
Molecular Diagnostic Techniques/methods

@article {pmid42100705,
year = {2026},
author = {Li, J and Liu, M and Yang, C and Fan, Z and Su, J and Hu, Y and Yang, Y and Li, J and Pu, Y and Ma, E and Deng, X and Sun, J},
title = {Preceding crops may reduce denitrification potential and enhance ammonium assimilation pathways.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808894},
pmid = {42100705},
issn = {1664-302X},
abstract = {BACKGROUND: Soil microorganisms are pivotal to nitrogen (N) cycling in croplands, yet how preceding crops modulate their functional profiles remains unclear.

OBJECTIVE: This field study aimed to quantify the effects of barley (BT) and rapeseed (RT) preceding crops (vs. no preceding crop, CK) on soil microbial functions and N-metabolic pathways in tobacco fields.

RESULTS: High-throughput metagenomics revealed that BT and RT significantly increased soil microbial richness (Chao1 index) compared to CK. At the genus level, CK contained 64% and 24% fewer unique taxa than BT and RT, respectively. While the top five KEGG functional pathways (e.g., Metabolic pathways, Biosynthesis of secondary metabolites) were conserved across treatments, their relative abundances differed. Critically, preceding crops reduced soil denitrification rates and increased glutamine dehydrogenase activity. Redundancy analysis confirmed that ammonium-N concentration was the key edaphic factor strongly correlated with microbial community structure and function (P < 0.01).

CONCLUSION: Our findings demonstrate that barley and rapeseed preceding crops enhance microbial richness and activity, thereby inhibiting denitrification and promoting N fixation via altered ammonium-N dynamics.},
}

@article {pmid42100978,
year = {2026},
author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD},
title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.},
journal = {Journal of biosciences},
volume = {51},
number = {},
pages = {},
pmid = {42100978},
issn = {0973-7138},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Female ; Rats ; Pregnancy ; Rats, Wistar ; *Malnutrition/metabolism/microbiology ; Docosahexaenoic Acids/administration & dosage/pharmacology ; Metabolome ; Fetal Development ; Male ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; *Prenatal Exposure Delayed Effects/metabolism ; Xanthophylls ; },
abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
Female
Rats
Pregnancy
Rats, Wistar
*Malnutrition/metabolism/microbiology
Docosahexaenoic Acids/administration & dosage/pharmacology
Metabolome
Fetal Development
Male
Metabolomics
Maternal Nutritional Physiological Phenomena
Dietary Supplements
*Prenatal Exposure Delayed Effects/metabolism
Xanthophylls

@article {pmid42100992,
year = {2026},
author = {Xu, X and Chen, D and Luo, N and Zhang, W and Lou, L},
title = {Metagenomic next-generation sequencing for pathology-suspected fungal infections at rare anatomical sites: a case series.},
journal = {Future science OA},
volume = {12},
number = {1},
pages = {2669032},
doi = {10.1080/20565623.2026.2669032},
pmid = {42100992},
issn = {2056-5623},
abstract = {OBJECTIVE: Histopathology for suspected fungal infections lacks species-level identification and is prone to morphological mimics. The utility of metagenomic next-generation sequencing (mNGS) at rare anatomical sites is underexplored.

METHODS: We retrospectively analyzed 10 cases with histopathology suggestive of fungal infection at rare sites (brain, cardiac valve, bone, etc.). All underwent mNGS testing on formalin-fixed paraffin-embedded samples.

RESULTS: mNGS detected fungal DNA in 8/10 cases (80%), providing species-level identification (e.g., Cryptococcus, Candida, Fusarium, Rhizopus, Histoplasma). Polymicrobial infections were identified in 70%. mNGS corrected two misdiagnoses: one confirmed neurocysticercosis; another revealed only bacteria in a suspected fungal lesion. Antimicrobial resistance genes (ErmB) were identified in two cases.

CONCLUSION: mNGS enhances diagnostic precision at rare sites by enabling species identification, uncovering polymicrobial infections, and correcting morphological misdiagnoses, supporting targeted therapy.},
}

@article {pmid42101034,
year = {2026},
author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM},
title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70354},
doi = {10.1111/1758-2229.70354},
pmid = {42101034},
issn = {1758-2229},
support = {NA19NOS4190106//Texas General Land Office/ ; },
mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Ecosystem ; },
abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.},
}

*Estuaries
*Fresh Water/chemistry/microbiology/virology
Salinity
*Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification
Temperature
Metagenomics
Ecosystem

@article {pmid42101202,
year = {2026},
author = {Yashar, M and Thigale, UY and Karakus, S},
title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001228},
pmid = {42101202},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.},
}

@article {pmid42101460,
year = {2026},
author = {Colmant, AMG and Parry, RH and Charrel, R and Coutard, B},
title = {Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences.},
journal = {The Journal of general virology},
volume = {107},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002254},
pmid = {42101460},
issn = {1465-2099},
mesh = {*Genome, Viral ; Phylogeny ; *Flaviviridae/classification/genetics/isolation & purification ; Genomics ; Metagenomics ; },
abstract = {Jingmenviruses are a group of viruses related to orthoflaviviruses characterized by a segmented genome and multipartite organization that have been detected worldwide in a wide range of hosts. With the growing number of new jingmenvirus sequences identified in metagenomics data, it can be difficult to assess whether a new sequence is associated with a new virus species or with a strain of an existing species. The ICTV is about to ratify the reclassification of the Flaviviridae family, recognizing segmented viruses previously designated jingmenviruses as part of that family and proposing two genera to classify them: Jingmenvirus and Guaicovirus. These proposals do not include clear criteria to classify jingmenviruses and related sequences into species or genera. In order to determine such criteria, we generated a large sequence database from published and newly assembled sequences. Indeed, we screened public raw sequencing data from studies that did not search for or report jingmenvirus or related sequences, looking for new strains of previously described viruses. We then performed multiple sequence alignments and used the inferred percentage identity values to determine demarcation criteria based on the distribution of evolutionary distances upon pairwise comparisons. We report the identification of almost 60 libraries containing jingmenvirus and related sequences, in a wide range of sample types and geographical locations. Using these data and published sequences, we have determined that to be classified as a virus species, at least four segments are required, on which eight cut-off values in percentage identity (nucleotide and amino acid) are used for demarcation. The use of these criteria would enhance consistency in jingmenvirus taxonomy and provide a standardized framework for comparative genomics studies of these viruses, as they are still under-characterized.},
}

*Genome, Viral
Phylogeny
*Flaviviridae/classification/genetics/isolation & purification
Genomics
Metagenomics

@article {pmid42101522,
year = {2026},
author = {Yuan, C and Zhang, T and Huo, J and Liang, W and Wang, L},
title = {Comparative analysis of next-generation versus third-generation sequencing for pathogen detection in clinical samples: a diagnostic accuracy study.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101522},
issn = {1573-0972},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Prospective Studies ; *Communicable Diseases/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Fungi/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; },
abstract = {BACKGROUND: The rapid and accurate identification of pathogens is crucial for clinical management of infectious diseases. While Next-generation sequencing (NGS) has transformed pathogen detection, Third-generation sequencing (TGS) offers advantages in real-time analysis and long-read capabilities. This study comprehensively compares the diagnostic performance of NGS and TGS across diverse clinical samples.

METHODS: We conducted a prospective diagnostic accuracy study involving 105 clinical samples (58 bronchoalveolar lavage fluid, 28 whole blood, 19 other body fluids) from patients with suspected infections. All samples were analyzed using both NGS (BGI platform) and TGS (Nanopore platform). Diagnostic performance was evaluated against a composite reference standard incorporating clinical diagnosis, microbiological culture, and laboratory findings.

RESULTS: NGS demonstrated significantly higher sensitivity compared to TGS (95.9% vs. 82.4%, p < 0.001), while TGS showed superior specificity (87.1% vs. 64.5%, p = 0.012). The overall agreement between platforms was 85.7% (Kappa = 0.702). NGS exhibited particular advantages in viral detection (32 vs. 8 detections, p < 0.001) and fungal identification (28 vs. 18 detections, p = 0.023), whereas both technologies showed comparable bacterial detection capabilities. The area under the ROC curve was 0.92 for NGS and 0.85 for TGS. Turnaround time was significantly shorter for TGS (median 8 h vs. 30 h, p < 0.001).

CONCLUSION: NGS and TGS demonstrate complementary strengths in clinical pathogen detection. NGS offers superior sensitivity and enhanced detection of viral and fungal pathogens, making it suitable for comprehensive diagnostic evaluation. TGS provides rapid results with higher specificity, advantageous for time-critical clinical decisions. A combined or scenario-specific approach may optimize pathogen detection in clinical practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
Prospective Studies
*Communicable Diseases/diagnosis/microbiology
*Bacteria/genetics/isolation & purification/classification
Viruses/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology/virology
Fungi/genetics/isolation & purification
*Molecular Diagnostic Techniques/methods

@article {pmid42101699,
year = {2026},
author = {Bharsakale, RD and Gubyad, MG and Jagannadham, PTK and Kokane, SB and Warghane, AJ and Kokane, AD and Ghosh, DK},
title = {Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101699},
issn = {1573-0972},
support = {Grant No. F.No. 16-11/PP/ICAR-CRP/25-26//ICAR- Consortium Research Platform on Vaccine and Diagnostics/ ; },
mesh = {*Citrus/microbiology ; India ; *Genome, Bacterial ; *Plant Diseases/microbiology ; *Rhizobiaceae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Whole Genome Sequencing ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Base Composition ; Liberibacter ; },
abstract = {Huanglongbing (HLB, 'Candidatus Liberibacter asiaticus') is one of the most devastating pathogens in citrus domain. Here, we present the nearly complete genome sequence of a CR-NGP1 strain obtained a from symptomatic Nagpur Mandarin (Citrus reticulata) tree in the Nagpur region of Central India. High-throughput sequencing on the Illumina NovaSeq 6000 platform generated ~ 85.7 million paired-end reads, 63.5 million paired-end reads and 14.8 million paired-end reads for sample CLas_001, CLas_002 and CLas_003 each with 150 bp read length, respectively. Two assembly strategies were used: (i) reference-based assembly with SPAdes produced a draft genome of ~ 1.19 Mb with assembly comprised 149 contigs, with an N50 of 14,173 bp, longest contig of 39,711 bp, and an overall GC content of 36.27%. (ii) KBase CONCOCT binning v1.1 applied to all 3 samples produced a nearly complete CR-NGP1 genome of ~ 1,156,009 bases with assembly of 93 contig, with an N50 of 17,668 bp, a longest contig of 39,711 bp, and an overall GC content of 36.4%. This resource of a CLas genome from Central India provides important insights to understand genetic diversity of CLas strains and will facilitate comparative genomics and epidemiological studies of Huanglongbing.},
}

*Citrus/microbiology
India
*Genome, Bacterial
*Plant Diseases/microbiology
*Rhizobiaceae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
Phylogeny
Whole Genome Sequencing
DNA, Bacterial/genetics
Sequence Analysis, DNA
Base Composition
Liberibacter

@article {pmid42101805,
year = {2026},
author = {Li, Q and Yang, X and Zhu, H and Yang, S and Yin, G},
title = {A rare case of long-standing lupus vulgaris with psoriasiform manifestations diagnosed by mNGS: a case report.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42101805},
issn = {1435-4373},
abstract = {This report describes a rare case of lupus vulgaris mimicking psoriasis, undiagnosed for over 40 years. Conventional diagnostics, including histopathology and mycobacterial culture, failed to yield a definitive diagnosis. Ultimately, metagenomic next-generation sequencing (mNGS) of the skin tissue detected the Mycobacterium tuberculosis complex, confirming the infection. The patient showed marked clinical improvement following two months of dual-drug anti-tuberculosis therapy. This case highlights the clinical utility of mNGS for diagnosing atypical, long-standing cutaneous tuberculosis when conventional methods are negative, thereby preventing prolonged misdiagnosis and ensuring timely treatment.},
}

@article {pmid42102564,
year = {2026},
author = {Long, Z and Zhang, B and Bing, H and Wu, Y},
title = {Identifying microbial candidates for assisted phytoremediation through long-term microbial succession and functional gene shifts across a 50-year chronosequence of vanadium-titanium magnetite tailings.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142304},
doi = {10.1016/j.jhazmat.2026.142304},
pmid = {42102564},
issn = {1873-3336},
abstract = {Soil microorganisms are central to vegetation restoration in metalliferous wastes. However, within mine tailings restoration chronosequences, particularly those enriched with vanadium (V), the long-term successional dynamics of microbial communities, their functional potentials, and the functional partitioning between key microbial taxa and lower-abundance microbial lineages remain poorly understood. Here, we utilized metagenomic sequencing across a 50-year restoration chronosequence to investigate changes in the microbial community and functional genes related to plant growth-promotion (phosphorus, nitrogen, and iron acquisition) and V tolerance/bioreduction. The results demonstrated significant shifts in the microbial community after five years of restoration. At the phylum level, Actinobacteria, Acidobacteria, Pseudomonadota, and Gemmatimonadota were dominant. In early stages (< 15 years), nitrogen and phosphorus acquisition genes (e.g., nif, fix, phoD) were 1.3-2.5 times more prevalent than in later stages, whereas functional genes associated with V (e.g., napA, narG, nirS) increased 1.5- to 2-fold over time. Vanadium and nitrogen were the primary environmental factors regulating both community structure and the relative abundance of critical functional genes. Keystone taxa possessed more nitrogen and phosphorus acquisition genes (65% and 45%, respectively), while metagenome-assembled genomes (MAGs) were enriched in genes related to siderophore biosynthesis (71%) and denitrification (potential V bioreduction) (65%). Based on functional gene profiles, Bradyrhizobium, Allosphingosinicella, Baekduia, Sphingomicrobium, and Hylemonella were identified as promising microbial candidates for enhancing restoration in V-contaminated sites. This study enables the development of targeted microbial consortia to mitigate nutrient deficiency and V toxicity, directly informing the design of more efficient, stage-specific phytoremediation strategies in V-rich tailings.},
}

@article {pmid42102590,
year = {2026},
author = {Feng, R and Wang, X and Zhang, X and Li, L and Gao, X and Li, J and Kang, J and Yu, X and Jia, S and Zheng, G and Shi, P},
title = {Hidden antibiotic resistance risks and key drivers during tertiary wastewater treatment deciphered by an integrated metagenomic framework.},
journal = {Environment international},
volume = {212},
number = {},
pages = {110281},
doi = {10.1016/j.envint.2026.110281},
pmid = {42102590},
issn = {1873-6750},
abstract = {Potential high-risk antibiotic resistance genes (ARGs) were considered as higher public health threats in wastewater treatment systems. While tertiary wastewater treatment processes (TWTPs) effectively remove conventional and emerging pollutants, their impact on ARGs with potential higher risk remains unclear. In this study, metagenomic assembly and binning were applied to profile potential-risk ARGs and identify key factors shaping their distribution during TWTPs. Results showed that potential-risk ARGs accounted for 34.32 ± 1.98% to 59.71 ± 1.55% of total ARGs, indicating their widespread persistence. Notably, DB significantly increased the relative abundance of potential-risk ARGs, particularly those conferring resistance to multidrug, bacitracin, and aminoglycoside. In parallel, DB treatment elevated the abundance of mobile genetic elements (MGEs), primarily transposase-related. DB treatment facilitated the co-occurrence of potential-risk ARGs and MGEs, especially multidrug and transposase/recombinase. Key bacterial hosts carrying potential-risk ARGs, such as Pseudomonas and Acinetobacter, were highly enriched after DB treatment, contributing substantially to the proliferation of these ARGs. In contrast, UV disinfection and CW treatment continuously reduced the abundance and risk levels of potential-risk ARGs, highlighting their complementary roles in mitigating antibiotic resistance risks during TWTPs. Variation partitioning analysis showed that bacterial community composition explained 36.15% of the variation in potential-risk ARG profiles, underscoring its primary role in ARG dynamics. Overall, this study provides genome-resolved insights into the hidden risks of ARGs and key drivers during TWTPs, highlights the necessity of optimizing operational parameters to mitigate antibiotic resistance dissemination.},
}

@article {pmid42102689,
year = {2026},
author = {Wang, W and Jiang, H and Liang, C and Yang, Y and She, D and Cheng, G and Wang, H},
title = {Soil functional carbon fraction accrual in temperate forests is linked to understory herbs, soil nutrients and microbial alterations.},
journal = {Journal of environmental management},
volume = {407},
number = {},
pages = {129886},
doi = {10.1016/j.jenvman.2026.129886},
pmid = {42102689},
issn = {1095-8630},
abstract = {Enhancing stable soil organic carbon (SOC) storage is vital for climate change mitigation. This study challenges the tree-centric paradigm in forest carbon management by investigating the relative roles of trees and understory herbs in driving SOC sequestration in temperate forests of Northeast China. Analyzing 720 soil samples from a 7.2 ha experimental forest, we measured oxidizable SOC fractions and tested the hypothesis that the understory herb layer is a primary driver of SOC accrual, mediated by soil properties and microbial communities. Results strongly supported our hypotheses. Plots with dense, tall herbs exhibited significantly higher levels of active and passive carbon fractions (increases of 7%-16%, amplified to 21%-45% when accounting for soil nutrients, physiochemistry, and water-holding capacity), whereas tree size showed no significant effect. Soil nitrogen was the strongest predictor of SOC variation. Herbs intensified the positive SOC-nitrogen relationship and were positively associated with beneficial soil conditions (e.g., near-neutral pH), contrary to the weak or negative correlations observed for trees. Structural equation modeling revealed that herbs exerted significant direct and indirect positive effects on carbon fractions, while the effects of trees were nonsignificant. Metagenomic analysis identified two contrasting microbial phyla groups: "positive-SOC" phyla (e.g., Thaumarchaeota, Planctomycetes) associated with herbs and high SOC, and "negative-SOC" phyla (e.g., Chloroflexi, Gemmatimonadetes). These findings underscore the critical, underappreciated role of the understory herb layer in SOC sequestration, mediated through soil nutrient enhancement, soil acidity, water retention, and shifts in microbial communities. Forest management strategies aiming to maximize carbon storage should prioritize herb layer conservation alongside tree layer considerations.},
}

@article {pmid42102934,
year = {2026},
author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J},
title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134810},
doi = {10.1016/j.biortech.2026.134810},
pmid = {42102934},
issn = {1873-2976},
abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.},
}

@article {pmid42102935,
year = {2026},
author = {Li, J and Wu, Y and Li, X and Gao, R and Chen, X and Zhang, S and Zhang, J and Zhang, L and Zhang, S and Peng, Y},
title = {Partial Denitrification-Mediated anammox Evolution in anoxic Compartments: Deciphering metabolic activity and microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134812},
doi = {10.1016/j.biortech.2026.134812},
pmid = {42102935},
issn = {1873-2976},
abstract = {The integration of partial denitrification (PD, NO3[-]→NO2[-]) with anaerobic ammonium oxidation (Anammox) in anoxic biofilm systems presents a transformative approach for enhanced nitrogen removal from municipal wastewater. Through a 7-month comparative analysis of spatially stratified anoxic zones in an anaerobic-anoxic-oxic bioreactor treating real wastewater (NH4[+]: 47.6 ± 4.7 mg N/L; COD: 154.8 ± 29.6 mg/L), this study achieved 71.8 ± 5.8% total nitrogen removal (effluent TN: 12.9 ± 3.9 mg N/L), aiming to propose optimization frameworks targeting biofilm carrier deployment in the anoxic zone. Test results showed that functional dominance partitioning emerged as a key determinant: the first anoxic zone (A1) exhibited peak anammox activity (0.034 kg N/m[3]/d) via rapid acetate-driven nitrate reduction, while the third zone (A3) sustained maximum Ca. Brocadia abundance (1.7%). Metagenomic sequencing further revealed that the highest ratio of NO3[-] reductase gene (narG) to NO2[-] reductase genes (nirS, nirK) was 2.06 in A3 compared to 1.39-1.68 in the other biofilms, indicating a stronger ability to supply NO2[-] to anammox. Carbon metabolic gene distribution revealed A1's acetate/glucose preference versus A3's endogenous metabolism dominance (elevated TCA cycle genes). This study proposes an innovative biofilm management framework for energy-efficient municipal wastewater treatment: front-positioned carriers maximize anammox nitrogen removal under moderate carbon-to-nitrogen ratios (3-5), while rear-positioned units secure anammox biomass retention during carbon surges.},
}

@article {pmid42102938,
year = {2026},
author = {Wu, Y and Yang, X and Deng, Y and Zhao, S and Wang, D and Zhang, W},
title = {Performance of microbial deodorization on anaerobically digested biosolids and odor rebound under rewetting conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134809},
doi = {10.1016/j.biortech.2026.134809},
pmid = {42102938},
issn = {1873-2976},
abstract = {Odor control is a critical bottleneck in the quality upgrade of anaerobically digested biosolids for land application. The efficacy of microbial deodorization on biosolids has been scarcely evaluated and the mechanisms behind remain unclear. This study applied a sensory-instrumental combined analysis approach to evaluate the deodorization efficiency of two microbial agents on biosolids and odor recurrence upon rewetting. Results show that treatment with microbial agent could reduce the odor intensity and mitigate ammonia emission, yet it failed to completely eliminate the odor. The volatile profile of biosolids is complex, including various N-, S-, O-containing organic and inorganic compounds that collectively contribute to the malodor of biosolids. Rewetting of biosolids induced a rapid odor rebound to varying degrees depending on the maturity of biosolids. Deodorization treatment enhanced the solubility, transformation of biosolids organic matter and increased the humic-like characteristics of WEOM and reshaped the bacterial community showing enrichment of functional taxa (e.g., Actinobacteriota and Chloroflexi). Metagenomic analysis revealed that the key nitrogen-cycling genes (ureC, narG) were suppressed, thereby limiting the generation of NH3 and other related odorants. These findings elucidate a mechanistic linkage between microbial dynamics and the odor generation potential of biosolids, and highlight the critical role of moisture management in governing odor generation and post-deodorization biological stability of biosolids.},
}

@article {pmid42102997,
year = {2026},
author = {Li, Y and Yu, T and Li, Z and Peng, J and Zhang, Y and Wang, Q and Xie, S},
title = {From high- to low-risk resistomes: Dynamic shifts in antibiotic resistance during biofilm development in a full-scale biological activated carbon fluidized bed.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128291},
doi = {10.1016/j.envpol.2026.128291},
pmid = {42102997},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in drinking water bioreactor biofilms pose significant public health risks, yet existing studies focus on mature biological activated carbon (BAC) biofilms, overlooking the early colonization stage critical for ARG origin and dissemination. This gap hinders understanding of ARG dynamics and resistance mechanisms during drinking water BAC biofilm development. Using metagenomics, we first systematically investigated ARG risk dynamics in a full-scale biological activated carbon fluidized bed (BACFB)-a state-of-the-art drinking water technology-across operational days 7-187. Microbial communities and ARG profiles clustered distinctively into early (days 7-37) and late (days 82-187) stages. Upon biofilm stabilization, total ARG abundance significantly decreased (P< 0.05), with high-mobility/high-risk ARGs (sulfonamide-, florfenicol-, aminoglycoside-type) replaced by low-mobility types (rifamycin-, fosfomycin-type). These shifts were correlated with reduced abundance of Pseudomonadota (P < 0.05), increasing trends in the abundance of Bacillota and Actinomycetota (P < 0.1), and decreased abundance of mobile genetic elements, particularly plasmids (P < 0.01). Pathogenic ARGs shifted from aminoglycoside/tetracycline to rifamycin, with Bacillus thuringiensis/Streptococcus pneumoniae (rphB-carrying) as key late-stage risks. Rank I/II and emerging ARGs (mcr, tet(X)) also declined. Our findings uncover the dynamics of ARG risks during BAC biofilm development and highlight the underlying ecological drivers, providing a robust scientific basis for targeted risk mitigation in drinking water treatment systems.},
}

@article {pmid42103024,
year = {2026},
author = {Zhang, T and Li, S and Wu, Y and Leung, J and Jiang, H and Xu, Z and Ng, SC and Kwok, T},
title = {Gut microbial signatures for aging-related sarcopenia and dietary links among community-dwelling old-old adults: A metagenomic study.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {113161},
doi = {10.1016/j.exger.2026.113161},
pmid = {42103024},
issn = {1873-6815},
abstract = {BACKGROUND AND OBJECTIVES: Sarcopenia, characterized by progressive loss of muscle mass, strength and function, poses a major aging-related health challenge. While a gut-muscle axis is implicated, microbiota-sarcopenia associations in the old-old (≥80 years) remain unexplored.

METHODS: This cross-sectional analysis included 315 community-dwelling adults aged ≥80 years from a longitudinal cohort at the 20-year follow-up timepoint, of whom 180 met the inclusion criteria. Gut microbiota was profiled by shotgun metagenomic sequencing alongside sarcopenia assessment. Microbial taxa associated with sarcopenia were identified using MaAsLin2, and dietary associations were assessed by partial Spearman correlation.

RESULTS: The prevalence of sarcopenia in this old-old cohort (mean age 86.8 ± 4.3 years) was 51.7%. Sarcopenic individuals showed lower nutrition scores, reduced microbial richness and altered β-diversity (all P < 0.05). Multivariable analysis identified six differentially abundant species associated with sarcopenia (FDR < 0.10), including two positively associated (Ruthenibacterium lactatiformans and Catenibacillus scindens), and four negatively associated (Phascolarctobacterium faecium, Pyramidobacter piscolens, Lacrimispora saccharolytica and Limosilactobacillus mucosae). Random forest and LEfSe analysis validated R. lactatiformans and P. faecium as the most discriminative signatures for sarcopenia. After adjusting for obesity, these signatures remained significant (P < 0.05). These alterations were linked to functional dysregulation, including increased purine degradation and reduced biotin biosynthesis potential. R. lactatiformans abundance negatively correlated with dietary maltose intake (P < 0.05).

CONCLUSION: In old-old adults, we identified distinct gut microbiota signatures associated with sarcopenia. R. lactatiformans and P. faecium emerged as candidate features. The dietary-microbiota correlations suggest potential nutrition strategies. These findings provide a basis for exploring microbiota-based approaches in advanced aging.},
}

@article {pmid42103277,
year = {2026},
author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X},
title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.015},
pmid = {42103277},
issn = {2090-1224},
abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.

METHODS: Here, we enrolled 206 young chest pain patients (18-45 years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.

RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.

CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.},
}

@article {pmid42103708,
year = {2026},
author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J},
title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72757-2},
pmid = {42103708},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.},
}

@article {pmid42103726,
year = {2026},
author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G},
title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72637-9},
pmid = {42103726},
issn = {2041-1723},
support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.},
}

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52250-y},
pmid = {42103925},
issn = {2045-2322},
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

@article {pmid41866358,
year = {2026},
author = {Deepthi, M and Vadakkadath Meethal, K},
title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41866358},
issn = {2045-2322},
abstract = {UNLABELLED: Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41440-3.},
}

@article {pmid41902972,
year = {2026},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S},
title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41902972},
issn = {1432-184X},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; },
abstract = {UNLABELLED: The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02712-7.},
}

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48529-9},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51914-z},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

@article {pmid42092708,
year = {2026},
author = {Ye, Y and Miao, H and Fang, W and Ni, J and Yang, K and Gu, P and Ren, X and Zhang, Z},
title = {Deciphering dual effects of humic substrates on anaerobic ammonium oxidation: from metabolic facilitation to systemic nitrogen flux interference.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134791},
doi = {10.1016/j.biortech.2026.134791},
pmid = {42092708},
issn = {1873-2976},
abstract = {Anaerobic Ammonium Oxidation (Anammox) is a promising strategy for nitrogen removal from landfill leachate due to its energy efficiency and independence from external carbon sources. However, continuous changes in recalcitrant organic compounds (i.e., fulvic acid (FA) and humic acid (HA)) at different landfill stages have potential effect on stability of anammox process. The present study systematically investigated the successive change of FA/HA concentrations and ratio that induced by different landfill age on anammox process in a laboratory-scale moving bed biofilm reactor operated over 200 days. Results showed a distinct dual-effect transition of FA and HA on the anammox process. 50-100 mg/L FA significantly improved nitrogen removal, achieving a peak total nitrogen removal efficiency (TNRE) of 91%. In contrast, the introduction of HA (100-200 mg/L) triggered a decline in TNRE to 80% and caused substantial nitrate (NO3[-]-N) accumulation. Microbial analysis revealed that FA-driven carbon abundance stimulated Candidatus Kuenenia and DNRA-functional Paracoccus and Bacillus, whereas HA suppressed DNRA bacteria in favor of nitrification. Metagenomic analysis showed that the electron shuttle and carbon source characteristics of FA enriched the relative abundance of energy metabolism genes (i.e., F-type ATPase) and quorum sensing genes (i.e., lamB), accelerating the anammox and denitrification process. However, HA interfered with the nitrogen metabolic flux via suppressing denitrification process (i.e., napA/B and nirS) and promoting nitrification genes (i.e., amoA and nxrA/B), leading to the accumulation of NO3[-]-N. These findings provide a mechanistic basis for optimizing anammox processes under varying humic substance conditions in landfill leachate treatment.},
}

@article {pmid42092716,
year = {2026},
author = {Chai, Z and Chen, H and Cui, J and Song, C and Zheng, Y and Li, Y and Gao, T and Zheng, M},
title = {Micromolar chlorate sensitivity of wastewater-associated comammox Nitrospira: Endogenous toxification mechanism and implications for nitrification management.},
journal = {Bioresource technology},
volume = {454},
number = {},
pages = {134789},
doi = {10.1016/j.biortech.2026.134789},
pmid = {42092716},
issn = {1873-2976},
abstract = {Chlorate (ClO3[-]) is widely employed as a specific inhibitor of nitrite-oxidizing bacteria (NOB) to differentiate the contributions of ammonia-oxidizing microorganisms (AOMs). However, the discovery of completed ammonia oxidizing (comammox) Nitrospira, which performs both ammonia and nitrite oxidation, challenges the assumed specificity of chlorate, raising the question of whether it also inadvertently inhibits the ammonia oxidation activity of comammox Nitrospira, potentially leading to an underestimation of total ammonia oxidation activity in mixed communities. This study investigates the inhibitory kinetics and mechanisms of chlorate on wastewater-associated comammox Nitrospira. Batch assays revealed that comammox ammonia oxidation was hypersensitive to chlorate, with a half-maximal inhibitory concentration (IC50) of 9.11 µM, orders of magnitude lower than canonical NOB inhibition levels. Metabolic assays showed that 10 μM chlorate reduced ammonia oxidation activity to 49.1% during exposure, with recovery requiring multiple cultivation cycles. Integrated metagenomic and meta-transcriptomic analyses uncovered an endogenous toxification mechanism: chlorate is reduced by nitrite oxidoreductase (NXR) to cytotoxic chlorite, which triggers the upregulation of chlorite dismutase (CLD) and reactive chlorine species (RCS) defense genes, ultimately leading to metabolic arrest. This study confirms the inhibitory effect of chlorate on comammox Nitrospira and deciphers its RCS-mediated mechanism, emphasizing the need for caution when using chlorate-based assays to assess ammonia oxidation activity and providing a theoretical basis for selectively suppressing comammox Nitrospira in WWTPs.},
}

@article {pmid42092717,
year = {2026},
author = {Fu, D and Ma, H and Zhang, J and Wang, H and Wu, Y and Ge, L and Fan, C and Wu, S and Zhang, S and Gao, H and Chen, Z},
title = {Interplay of quorum-sensing signals (homoserine lactone/penicillic acid) and nitrate in regulating microbial processes: As(III) immobilization, CH4 and N2O emission in constructed wetlands.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134788},
doi = {10.1016/j.biortech.2026.134788},
pmid = {42092717},
issn = {1873-2976},
abstract = {The concurrent mitigation of arsenic (As) pollution and greenhouse gas (GHG) emissions in constructed wetlands represents a significant challenge, largely due to the complex interactions within microbial-driven elemental cycles. This study investigated the regulatory roles of distinct quorum-sensing (QS) signals, i.e., C4-homoserine lactone (C4-HSL, a promoter) and penicillic acid (PA, a quencher), in concert with nitrate on the microbial-mediated transformation of As and GHGs (CH4 and N2O) in flooded paddy soil microcosms. The results revealed that the nitrate + C4-HSL treatment concurrently enhanced As(III) immobilization (increased by 8%) while suppressing CH4 and N2O emissions (by 7% and 56%) over a 24-day incubation period, compared to nitrate alone. Conversely, the nitrate + PA treatment inhibited As(III) oxidation (∼17.6 µM residual As(III) leaching) and promoted the accumulation of GHGs (increasing CH4 and N2O emissions by 8% and 77%). Mechanistically, C4-HSL activated the complete QS signaling network under nitrate amendment. This activation led to the enrichment of key functional microbial consortia (e.g., Pseudogulbenkiania, Streptomyces and Alicyclobacillus), an increase in relative abundance of critical metabolic genes (e.g., aox, pmo, nosZ, cpaF, tadA and cco), stimulated the secretion of protein-rich extracellular polymeric substances, and enhanced overall electron transfer system activity. These coordinated changes fostered coupled biogeochemical processes such as Fe(II)/Mn(II)-coupled denitrification and denitrifying AOM. In contrast, PA disrupted native QS communication, suppressed the aforementioned functional microbial groups and altered biofilm composition. Overall, the application of specific QS signals with nitrate exhibits the potential to directionally steer microbial community function, thereby highlighting a promising microbial-level strategy for the co-management of As and GHGs in engineered wetland systems.},
}

@article {pmid42092753,
year = {2026},
author = {Palanisamy, M and Babalola, OO and Ramalingam, S},
title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42092753},
issn = {2730-6844},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; },
abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.},
}

*Salvia officinalis/microbiology
*Plant Leaves/microbiology
*Metagenomics
*Endophytes/genetics/classification
*Microbiota
*Metagenome
Bacteria/genetics/classification
Fungi/genetics

@article {pmid42093069,
year = {2026},
author = {Yuan, J and Li, J and Jin, L and Ye, J and Zhang, Z},
title = {Human herpesvirus-6B infection leading to hemophagocytic lymphohistiocytosis in an adult: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-06071-2},
pmid = {42093069},
issn = {1752-1947},
abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) secondary to human herpesvirus-6B (HHV-6B) infection is rare in immunocompetent adults.

CASE PRESENTATION: We report the case of a 43-year-old East Asian (Chinese) woman who developed HLH, presenting with persistent fever, jaundice, and cytopenias. Metagenomic next-generation sequencing (mNGS) identified HHV-6B in both peripheral blood and liver tissue, thereby establishing the etiologic diagnosis. Prompt initiation of antiviral therapy with ganciclovir, combined with corticosteroids and intravenous immunoglobulin, resulted in rapid clinical remission.

CONCLUSIONS: This case highlights the critical importance of early pathogen identification using mNGS and timely immunomodulatory treatment for improving outcomes in adult patients with virus-associated HLH.},
}

@article {pmid42093272,
year = {2026},
author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q},
title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0652},
pmid = {42093272},
issn = {2095-3941},
support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; },
abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.

METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.

RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.

CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.},
}

@article {pmid42093327,
year = {2026},
author = {Wang, S and Li, S and Lyu, H and Zhi, W and Dang, Z and Guo, R and Zhu, X and Ji, G},
title = {Quantifying the Contribution of Cryptic Sulfide-Driven Autotrophic Denitrification to N2O Production in a Seasonally Hypoxic River-Reservoir System.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03313},
pmid = {42093327},
issn = {1520-5851},
abstract = {Sulfur-autotrophic denitrification (S-ADN) has been frequently reported in inland waters, yet its quantitative contribution to nitrous oxide (N2O) productions remains poorly constrained. By combining field sampling, enrichment cultures, stable isotopes, and metagenomic analysis, we quantified S-ADN-derived N2O productions in an oligotrophic river-reservoir system and validated the universality of our approach across diverse aquatic ecosystems. A Thiobacillus-dominated S-ADN enrichment culture was successfully established over 218 days of continuous supplementation with reduced sulfur compounds, yielding critical isotopic signatures for source partitioning (δ[15]N[Bulk], average N isotopic composition; δ[18]O; and δ[15]N[SP], site preference). Then, the multi-isotope Bayesian model revealed that S-ADN (14.8%) and nitrifier denitrification (NDN, 21.1%) rapidly occupied the ecological niche of heterotrophic denitrification (HDN, 8.6%) to total microbial N2O sources under organic carbon-limited conditions. The cryptic sulfur cycle supplies a considerable pool of electron donors for S-ADN under low-sulfide conditions. Autotrophic denitrifiers (e.g., Thiobacillus, Sulfuritalea) exhibited significant synergistic interactions with ammonia-oxidizing archaea (AOA, Nitrosarchaeum), while ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira) jointly completed nitrification─with Nitrosomonas further competing for nitrite to drive NDN. This study advances the quantitative assessment of S-ADN's role in N2O production and provides novel insights into microbial community interactions in oligotrophic aquatic systems.},
}

@article {pmid42093770,
year = {2026},
author = {Niu, S and Guo, L and Li, Z and Liu, Y and Zhao, L},
title = {Clinical utility of metagenomic next-generation sequencing in the diagnosis of severe influenza complicated by invasive pulmonary aspergillosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1746504},
pmid = {42093770},
issn = {2235-2988},
mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Influenza, Human/complications/diagnosis ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Mannans/blood ; Galactose/analogs & derivatives ; Aged ; ROC Curve ; Adult ; China ; },
abstract = {OBJECTIVE: The incidence and mortality of severe influenza complicated by invasive pulmonary aspergillosis (IPA) have risen markedly in recent years. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for detecting IPA in patients with severe influenza.

METHODS: Severe influenza patients with suspected of having IPA admitted to Xinxiang Central Hospital, Henan Province, China, from March 2020 to September 2025 were retrospectively enrolled. Bronchoalveolar lavage fluid (BALF) and blood were collected for fungal culture, galactomannan (GM) assay, and mNGS. Final classification into IPA and non-IPA groups was based on composite clinical and microbiological criteria. Sensitivity, specificity, and receiver operating characteristic curves were used to compare the diagnostic performance of the three methods.

RESULTS: Comparison with traditional fungal culture and GM testing, mNGS provided significantly faster results. Among 189 patients suspected of severe influenza-associated IPA, mNGS demonstrated a sensitivity of 72.1% and a specificity of 80.2%. Its sensitivity was higher than that of fungal culture (28.6%), serum GM testing (37.6%), and BALF GM testing (44.1%); however, its specificity was slightly lower than that of fungal culture (89.5%), serum GM testing (84.3%), and BALF GM testing (81.3%). The area under the ROC curve (AUC) for mNGS was 0.76, which is higher than that for BALF GM testing (0.63), serum GM testing (0.61), and fungal culture (0.59). The combined diagnostic approach yielded an AUC of 0.83.

CONCLUSION: mNGS offers a rapid, sensitive and accurate solution for invasive pulmonary aspergillosis in severe influenza patients. It outperforms conventional fungal culture and galactomannan assays. Integrating mNGS with traditional diagnostic methods could substantially improve early detection and overall yield of IPA.},
}

Humans
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Influenza, Human/complications/diagnosis
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity
*Metagenomics/methods
Mannans/blood
Galactose/analogs & derivatives
Aged
ROC Curve
Adult
China

@article {pmid42094492,
year = {2026},
author = {Shan, Y and Pucci, N and Berns, C and Hoogendijk, R and Beijnvoort, M and Li, S and Sánchez-Cano, A and Kramer, G and Du, W and Mende, DR and Jan van Dijk, AD and Wortel, M and Zhang, J},
title = {A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.718440},
pmid = {42094492},
issn = {2692-8205},
abstract = {Human milk oligosaccharides (HMOs) are abundant and structurally diverse glycans that shape the development of infant gut microbiota. Yet, how individual HMOs and bacterial genes drive the community assembly remain elusive. Here, we reconstructed an eight-member infant Bacterial Community (iBaCo) from representing dominant taxa in human infant feces. When individual HMOs were the sole carbohydrate source, they showed deterministic effects on the iBaCo composition and metabolic output. Notably, the tetramer HMO lacto-N-tetraose (LNT), in spite of its identical monomer composition as lacto-N-neotetraose (LNnT), showed a strong effect on maintaining Bifidobacterium breve abundance in iBaCo, whereas LNnT did not. Monoculture growth profiling, proteomics, enzymatic kinetic assay, and molecular docking revealed that β -galactosidase D4BMY8 and the relevant downstream pathways are induced by LNT and that D4BMY8 has substrate preference on LNT over LNnT, enabling a faster growth of Bi. breve and accumulation of acetate and lactate in LNT compared to LNnT. Metabolic flux analysis indicated that the substrate-preference of β -galactosidase D4BMY8 drives the skewed energy cost toward lactate/acetate metabolic output. Finally, the D4BMY8-encoding gene lacZ5 is widely spread in all isolated Bi. breve genomes, but divergently distributed in infant metagenome-assembled Bi. breve genomes. Together, we demonstrated that a single enzyme-substrate interaction could orchestrate the composition and metabolic function of an infant bacterial community, which may contribute to the assembly of dynamic infant gut microbiota. Our integrative approach provides a mechanistic framework for understanding the interaction between diet, microbial community, and infant gut health.},
}

@article {pmid42094499,
year = {2026},
author = {Majidian, S and Chalco, A and Zheng, X and Webby, RJ and Bowman, AS and Poulson, RL and Nemeth, NM and Sedlazeck, FJ and Agustinho, DP},
title = {Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721707},
pmid = {42094499},
issn = {2692-8205},
abstract = {Phylogenomic surveillance is limited not by sequencing throughput, but by the difficulty of converting heterogeneous raw data into reliable evolutionary inference, particularly for low-titer and contaminated viral field samples. Here we present Omni2Tree, an assembly-free framework that reconstructs viral phylogenies directly from raw sequencing reads and generates easily shareable interactive reports and genome-wide entropy profiles to identify diversification. In H5N1 benchmark analyses, Omni2Tree maintained accurate placement and topological stability even under low coverage, unlike assembly or reference based methods. Omni2Tree generated an annotated phylogeny for 64-sample H5N1 field surveillance dataset from the eastern USA in under 3 hours. Omni2Tree recovered known phylogenetic structure and key variability insights across 1,328 hepatitis C virus and 707 human cytomegalovirus datasets, and resolved co-infecting respiratory viruses in clinical metagenomic samples. By enabling direct analysis from raw reads, Omni2Tree supports faster, more portable, and more decentralized phylogenomic surveillance across outbreak, clinical, and resource-limited settings.},
}

@article {pmid42094537,
year = {2026},
author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J},
title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721577},
pmid = {42094537},
issn = {2692-8205},
abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.},
}

@article {pmid42094770,
year = {2026},
author = {Tekere, M and Kalu, CM},
title = {Relative abundance of heavy metal resistance genes of three drinking water treatment plants unveiled through shotgun metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822428},
pmid = {42094770},
issn = {1664-302X},
abstract = {INTRODUCTION: The occurrence and abundance of heavy metal resistance genes (HMRGs) in drinking water treatment plants (DWTPs) and the stages at which they occur are a global challenge due to the risk of consuming contaminated water.

METHODS: The present study identified HMRGs associated with raw water sources, treatment stages (disinfection and filtration), final treated water, and produced sludge in three DWTPs across three provinces (Gauteng, Limpopo, and Mpumalanga) in South Africa, using a shotgun metagenomic approach.

RESULTS: In total, five classes of heavy metals (copper, arsenic, mercury, chromate, silver) and 50 resistance genes were identified across the three DWTPs. Most of the genes were obtained from the disinfection stages of the DWTPs.

DISCUSSION: This genomic dataset provides valuable information on the impact of disinfection stages on the relative abundance of HMRGs in drinking water treatment processes. Additionally, the transfer of genes into the final treated water consumed by the populace is a significant human health concern.},
}

@article {pmid42094845,
year = {2026},
author = {Olson, N and Thystrup, CAN and Smith, F and Mucache, H and Fafetine, J and Saíde, J and Mondlane-Milisse, A and Brito, DRA and Jesser, KJ and Brown, J and Hald, T and Freeman, M and Levy, K and Nadimpalli, ML},
title = {Strain-level analyses of public sequencing data to characterize Escherichia coli strain sharing between children and chickens in Mozambique.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101429},
pmid = {42094845},
issn = {2352-7714},
abstract = {Escherichia coli causes diarrhea in children and can be transmitted from animals. Characterizing the scope of human-animal strain sharing is crucial for assessing potential health risks; however, conventional methods that assess single isolates are resource-intensive and lack sensitivity. Strain-level metagenomic analyses can reveal within-host strain diversity and between-host strain sharing. In this study, we aimed to determine whether E. coli strains we previously detected among chickens in Mozambique might pose meaningful risks to local children. To achieve this, we compared E. coli strains in chicken metagenomes to E. coli strains reported by others in children's stool in the same community during the same period (2014-2022) using the Strain Genome Explorer toolkit. At least one E. coli strain was shared between 37/23,937 (0.15%) chicken-human pairs. This approach represents a novel method for assessing the scope of bacterial strain sharing between human and animal populations within a community.},
}

@article {pmid42094906,
year = {2026},
author = {Zeng, Q and Xie, L and Dai, W and Xu, F and Dai, Y},
title = {Extracorporeal Membrane Oxygenation Haemoperfusion for Leptospirosis Pulmonary Hemorrhagic Disease: Report of 1 Case.},
journal = {Respirology case reports},
volume = {14},
number = {},
pages = {e70565},
pmid = {42094906},
issn = {2051-3380},
abstract = {Severe pulmonary leptospirosis (SPFL), characterized by diffuse alveolar haemorrhage (DAH) and acute respiratory distress syndrome (ARDS), carries a high mortality, often due to diagnostic delays and complex management. We report a case of a 42-year-old male with outdoor occupational exposure who presented with fever and hemoptysis, rapidly progressing to severe respiratory failure and thrombocytopenia. Chest imaging confirmed DAH/ARDS. For refractory hypoxemia, veno-venous extracorporeal membrane oxygenation (VV-ECMO) was initiated without systemic anticoagulation due to active pulmonary haemorrhage. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid rapidly identified Leptospira interrogans, enabling targeted antimicrobial therapy alongside multidisciplinary support. The patient gradually improved, was successfully weaned from ECMO and ventilator support, and was discharged without residual organ dysfunction. This case demonstrates that early application of anticoagulation-free VV-ECMO combined with mNGS-based rapid diagnosis and multidisciplinary care can improve outcomes in SPFL, highlighting the importance of considering this diagnosis in febrile patients with DAH and environmental exposure.},
}

@article {pmid42094994,
year = {2026},
author = {Vasselin, A and Scavazzin, V and Talarmin, JP and Lamoureux, C and Pérès, M and Le Bars, H and Fangous, MS and Beauruelle, C and Ansart, S and Héry-Arnaud, G},
title = {Granulicatella adiacens infective endocarditis in pregnancy: diagnostic contribution of metagenomic sequencing-a case report.},
journal = {ASM case reports},
volume = {2},
number = {3},
pages = {},
pmid = {42094994},
issn = {2996-2684},
abstract = {BACKGROUND: Granulicatella adiacens is a fastidious Gram-positive coccus and is a rare but recognized cause of infective endocarditis. Infective endocarditis during pregnancy is uncommon but carries substantial maternal and fetal risk. Plasma metagenomic analysis of microbial cell-free DNA has emerged as a complementary diagnostic tool in culture-negative infections.

CASE SUMMARY: We describe a 35-year-old pregnant woman with known mitral valve prolapse who presented at 21 weeks of gestation with an acute ischemic stroke. Initial etiological work-up, including transesophageal echocardiography, was unremarkable. Ten days later, she re-presented with left-arm pain and neurologic symptoms. Repeat echocardiography revealed multiple mitral vegetations compatible with infective endocarditis. Despite multiple sets of prolonged-incubation blood cultures and extensive serological testing, all microbiological investigations remained negative. Empirical intravenous ceftriaxone was initiated based on the working diagnosis of HACEK endocarditis. A plasma metagenomic cell-free DNA test ultimately identified G. adiacens, which was suspected to have entered the body through dental treatment received a few weeks earlier. Ceftriaxone was continued given the favorable clinical response, with vegetation resolution, troponin decline, and uncomplicated term delivery of a healthy infant.

CONCLUSION: This case illustrates the diagnostic challenges of culture-negative infective endocarditis in pregnancy and underscores the value of plasma microbial cell-free DNA sequencing as a complementary tool when conventional methods fail. It also emphasizes the need to repeat echocardiography when clinical suspicion remains high and raises the question of antibiotic prophylaxis for high-risk dental procedures in pregnant women with underlying valvular heart disease.},
}

@article {pmid42095002,
year = {2026},
author = {de Araújo Butarelli, AC and Peres, FV and Pellizari, VH and Bendia, AG},
title = {Hot life in Antarctica: a novel metabolically versatile Pyrodictiaceae genus thriving at a volcanic-cryosphere-marine interface.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag080},
pmid = {42095002},
issn = {2730-6151},
abstract = {Deception Island fumaroles in Antarctica represent rare environments where extreme heat intersects with cryospheric and marine conditions, creating remarkable environmental gradients. From the near-boiling sediments, we reconstructed a high-quality metagenome-assembled genome affiliated with the Pyrodictiaceae. Phylogenomic analyses revealed that this genome, proposed to represent Ca. Pyroantarcticum pellizari, forms a distinct lineage separated from known genera in the family. Functional annotation uncovered a versatile metabolic repertoire, including pathways for sulfur and nitrogen cycling, peptide and amino acid transport, and mixotrophic energy conservation. Stress-response systems such as reverse gyrase, thermosome, and small heat-shock proteins were complemented by lineage-specific genes related to membrane stability, metal detoxification, and Pyrodictiaceae-specific cannulae. These adaptations likely support survival under sharp temperature gradients, hydrogen sulfide emissions, and high metal concentrations at the volcanic-cryosphere-marine interface. Our findings expand the phylogenetic and ecological scope of Pyrodictiaceae, highlighting Antarctic marine volcanoes as unique refuges for hyperthermophiles and as valuable models for investigating life's habitability under extreme temperatures.},
}

@article {pmid42095017,
year = {2026},
author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X},
title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1768985},
pmid = {42095017},
issn = {2297-1769},
abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.},
}

@article {pmid42095439,
year = {2026},
author = {Williams, TGS and Umpleby, H and Fisayo, T and Rampling, T and Houlihan, CF},
title = {Clinician perspectives on patient consent for metagenomic next-generation sequencing of blood samples for the diagnosis of infection in clinical practice.},
journal = {Journal of medical microbiology},
volume = {75},
number = {5},
pages = {},
doi = {10.1099/jmm.0.002164},
pmid = {42095439},
issn = {1473-5644},
mesh = {Humans ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; *Informed Consent ; Surveys and Questionnaires ; United Kingdom ; *Communicable Diseases/diagnosis/blood ; },
abstract = {Introduction. Pathogen diagnostics based on metagenomic next-generation sequencing (mNGS) are now in clinical use. mNGS can identify unexpected pathogens or organisms of unclear significance and generate human genomic data. Given these features, it has been suggested that patients should provide specific informed consent for mNGS.Gap Statement. There is limited published guidance on the appropriate form of consent for clinical infectious disease mNGS to guide clinical implementation and current practice varies.Aim. To inform a pilot of mNGS for returning travellers delivered at a reference laboratory for use by specialist infection clinicians, we sought clinician perspectives on the form of consent required for mNGS and the information patients require to make an informed decision.Methodology. A national survey of infection specialists provided clinicians' opinions.Results. If consent for an infection screen including blood-borne virus testing had already been provided, only a minority of surveyed clinicians (22 out of 124, 18%) thought that mNGS should be discussed before it was performed on pre-existing blood samples.Conclusion. Most of the UK infection clinicians surveyed did not think that mNGS of blood from returning travellers required discussion before being performed when patients had already consented for infection diagnostics to find the cause of their illness. However, clinicians felt that patients should be aware of the potential for additional testing and wanted information on mNGS to be readily available.With the increasing availability of clinical infectious disease mNGS, engagement of non-specialist clinicians and patients is required to confirm the generalizability of these perspectives. The model of consent used for clinical infectious disease mNGS should be ethically adequate in addition to being acceptable to patients and clinicians.},
}

Humans
*Metagenomics
*High-Throughput Nucleotide Sequencing
*Informed Consent
Surveys and Questionnaires
United Kingdom
*Communicable Diseases/diagnosis/blood

@article {pmid42095681,
year = {2026},
author = {Muthamilselvi Sivabalan, SK and Vijayakumar, V and Sengupta, P and Palmal, S and Krishnamurthi, S and Kumar Singh, N and Kyrpides, NC and Raman, K and Venkateswaran, K},
title = {Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0127325},
doi = {10.1128/spectrum.01273-25},
pmid = {42095681},
issn = {2165-0497},
abstract = {NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.},
}

@article {pmid42096004,
year = {2026},
author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X},
title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {42096004},
issn = {2523-899X},
abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.

METHODS: Women with SA (n = 30) and those with normal early pregnancy (NP, n = 28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.

RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1β and TNF-α (1.49-fold and 1.51-fold, both P < 0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-κB signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score > 2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP > 1.0, adjusted P < 0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P < 0.0001) in the decidual tissue of SA patients.

CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.},
}

@article {pmid42096148,
year = {2026},
author = {Zhu, D and Wang, S and Sun, X and Britton, RA},
title = {CRISPR-AsCas12a and dAsCas12a-Mediated Gene Knockout and Knockdown in Clostridioides difficile.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3046},
number = {},
pages = {47-55},
pmid = {42096148},
issn = {1940-6029},
mesh = {*Clostridioides difficile/genetics ; *CRISPR-Cas Systems/genetics ; Gene Editing/methods ; *Gene Knockout Techniques/methods ; *Gene Knockdown Techniques/methods ; Bacterial Proteins/genetics ; CRISPR-Associated Proteins/genetics ; },
abstract = {Clostridioides difficile (C. difficile) is a leading cause of antibiotic-associated diarrhea and severe colitis, yet its genetic manipulation has long been constrained by low DNA transfer efficiency and limited recombination systems. Recent advances in CRISPR-based technologies have revolutionized the genetic toolkit for this pathogen, enabling precise genome editing and transcriptional regulation. Among CRISPR nucleases, Cas12a offers distinct advantages over Cas9 for bacterial applications, including a smaller size, T-rich PAM recognition, single-crRNA requirement, and reduced toxicity, which enhances conjugation efficiency in genetically recalcitrant organisms. AsCas12a-based platforms have enabled large fragment deletions, multiplex editing, and rapid generation of marker-free mutants in C. difficile. Complementing these nuclease-active systems, nuclease-deactivated variants (dCas9 or dAsCas12a) support CRISPR interference (CRISPRi)-a reversible, tunable approach for transcriptional repression without altering genomic sequences. Compared to traditional mutagenesis, CRISPRi greatly accelerates functional genomics by enabling high-throughput screening and drug target discovery. Together, our lab has independently developed CRISPR-AsCas12a-mediated genome editing and dAsCas12a-based CRISPRi tools, providing complementary strategies to overcome longstanding genetic barriers in C. difficile. These tools open new avenues for system-level interrogation of virulence, antibiotic resistance, and host-pathogen interactions.},
}

*Clostridioides difficile/genetics
*CRISPR-Cas Systems/genetics
Gene Editing/methods
*Gene Knockout Techniques/methods
*Gene Knockdown Techniques/methods
Bacterial Proteins/genetics
CRISPR-Associated Proteins/genetics

@article {pmid42096157,
year = {2026},
author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM},
title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3046},
number = {},
pages = {171-187},
pmid = {42096157},
issn = {1940-6029},
mesh = {*Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism/chemistry ; Bacterial Adhesion ; Bioreactors/microbiology ; *Plankton ; Intestinal Mucosa/microbiology ; Hydrogels/chemistry ; Biofilms/growth & development ; },
abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.},
}

*Clostridioides difficile/physiology
*Gastrointestinal Microbiome
Humans
Mucins/metabolism/chemistry
Bacterial Adhesion
Bioreactors/microbiology
*Plankton
Intestinal Mucosa/microbiology
Hydrogels/chemistry
Biofilms/growth & development

@article {pmid42096470,
year = {2026},
author = {Hardick, J and Anantharam, R and Lu, J and Salzberg, SL and Rothman, RE and Fenstermacher, KZJ and Pekosz, A and Onzia, A and Nakiyingi, L and Manabe, YC and Kandathil, AJ},
title = {Comparison of unbiased metagenomic next generation sequencing to targeted multiplex diagnostic assays for the detection of respiratory viruses.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0347750},
doi = {10.1371/journal.pone.0347750},
pmid = {42096470},
issn = {1932-6203},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; Male ; Female ; Adult ; Nasopharynx/virology ; Middle Aged ; Multiplex Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics/isolation & purification ; *RNA Viruses/genetics/isolation & purification ; Aged ; Child, Preschool ; Adolescent ; Child ; Young Adult ; },
abstract = {OBJECTIVES: Accurate diagnosis of existing and emerging respiratory pathogens is important. We evaluated the capability of unbiased metagenomic next generation sequencing (mNGS) to identify pathogenic RNA viruses from two cohorts of nasopharyngeal (NP) swabs previously tested by commercial multiplex respiratory diagnostics.

METHODS: NP swabs (N = 100) in viral transport media (VTM) were assessed using mNGS for this study. Cohort 1 (N = 52) consisted of symptomatic individuals who tested negative for SARS-CoV-2, influenza A/B, and RSV by the Xpert Xpress CoV-2/Flu/RSV Plus multiplex respiratory virus panel and were tested by mNGS for undetected pathogens. Cohort 2 (N = 48) included symptomatic individuals who were positive (N = 26) or negative (N = 22) by the ePlex RP2 multiplex respiratory pathogen panel. Samples were positive for influenza A (N = 8), rhinovirus/enterovirus (N = 5), RSV (N = 4), adenovirus (N = 3), parainfluenza (N = 2), seasonal coronaviruses (N = 2), and human metapneumovirus (N = 1), as well as a rhinovirus/enterovirus/human metapneumovirus co-infected sample (N = 1). mNGS results were compared with ePlex RP2 findings, and symptomatic negative samples were evaluated for additional pathogen detection.

RESULTS: Cohort 1 contained 8% (4/52) viral and 19% (10/52) bacterial reads. In cohort 2, positive concordance between ePlex RP2 and mNGS was 31% (8/26). mNGS did not identify any viral reads in ePlex RP2-negative samples. However, it detected other microbial reads, such as Acanthamoeba castellanii, in 21% (10/48) of samples.

CONCLUSION: In this study, targeted multiplex amplification methods demonstrated better overall sensitivity in NPs of symptomatic respiratory individuals than mNGS. Other mNGS approaches may produce different results. This study suggests that mNGS may offer adjunctive information, including the detection of rare pathogens, which may be helpful in some clinical contexts.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Respiratory Tract Infections/virology/diagnosis
Male
Female
Adult
Nasopharynx/virology
Middle Aged
Multiplex Polymerase Chain Reaction/methods
SARS-CoV-2/genetics/isolation & purification
*RNA Viruses/genetics/isolation & purification
Aged
Child, Preschool
Adolescent
Child
Young Adult

@article {pmid42096522,
year = {2026},
author = {Zhao, D and Zhang, C and Li, M and Li, H and Su, S and Zhang, X},
title = {Characteristics of carbon-fixing microbial communities and pathways across different aquatic systems in the Tianjin Binhai region.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag112},
pmid = {42096522},
issn = {1365-2672},
abstract = {AIMS: Microbial carbon fixation is central to carbon cycling and carbon sink functioning in coastal aquatic ecosystems. Although carbon fixation pathways have been increasingly investigated across diverse aquatic environments, comparative evidence remains limited for hydrologically connected yet hydrochemically contrasting coastal groundwater and surface water systems. This study aimed to compare carbon-fixation-associated microbial communities and major carbon fixation pathways across groundwater, river water and reservoir water in the Tianjin coastal region.

METHODS AND RESULTS: We integrated metagenomic sequencing with hydrochemical analyses to characterise carbon-fixation-associated microbial communities and six representative carbon fixation pathways. Surface waters were dominated by bacteria and showed relatively stable community composition, whereas groundwater communities comprised both bacteria and archaea and displayed pronounced spatial heterogeneity. The Calvin-Benson-Bassham cycle was prevalent across all water types, and the reductive tricarboxylic acid (rTCA) cycle was also widely distributed. Groundwater showed higher contributions of the Wood-Ljungdahl pathway, the archaeal 3-hydroxypropionate/4-hydroxybutyrate and dicarboxylate/4-hydroxybutyrate cycles, together with the rTCA cycle, indicating coexisting carbon fixation strategies. Pathway abundance and module completeness further suggested differences in pathway integrity among water types. Total dissolved solids, HCO3⁻, CO32⁻ and dissolved organic carbon were key correlates of carbon fixation gene distribution.

CONCLUSIONS: Carbon-fixation-associated microbial communities, pathway distributions, and pathway integrity differed markedly between coastal groundwater and surface waters. Groundwater exhibited enhanced non-CBB cycle potentials and more diversified carbon fixation strategies, highlighting the importance of groundwater processes in evaluating carbon sequestration potential and carbon cycling in hydrochemically heterogeneous coastal aquatic systems.},
}

@article {pmid42096753,
year = {2026},
author = {Jin, B and Bai, Z and Yan, Y and He, H and Du, J and Xu, Y and Wang, L and Ji, J},
title = {Antibiotic-driven mechanisms in endogenous partial denitrification (EPD): Nitrite accumulation, microbial adaptation, functional gene responses and resistance gene proliferation.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142257},
doi = {10.1016/j.jhazmat.2026.142257},
pmid = {42096753},
issn = {1873-3336},
abstract = {The mechanisms by which antibiotics affect Endogenous Partial Denitrification (EPD) systems remain unclear. This study investigated the relationships between antibiotic type and pollutant removal, along with the underlying microbial metabolic mechanisms in an EPD system exposed to three antibiotics. The results showed that sulfadiazine (SD) and sulfamethoxazole (SMZ) exhibited higher chemical oxygen demand removal efficiency than tetracycline (TC). In the SD system, NO3[-]-N removal was 84.13%, whereas other systems achieved 97%, which was associated with a higher abundance of the n arG and nirS. Proteobacteria and Chloroflexi demonstrated strong adaptability to the antibiotics. TC inhibited the tricarboxylic acid cycle and organic matter degradation may be related to the reduced mdh. SD induced microorganisms to convert carbon sources into polyhydroxybutyrate instead of utilizing them directly, while SMZ optimized nitrogen metabolism by increasing the abundance of nirS and nirK, leading to higher NO2[-]-N accumulation in these two EPD systems. SD stress reduced the abundance of ppk2/ppx gene, inhibited the energy production and internal carbon reserve of denitrifying polyphosphate-accumulating organisms in anaerobic stage. Although the microorganisms had stronger phosphorus uptake potential by up-regulating ppk1 gene, the lack of ATP necessary to drive this process eventually led to the reduction of PO4[3] [-]-P removal ability. The abundance of resistance genes peaked in the SD system, significantly increasing the risk of antibiotic resistance. This study deciphers the metabolic mechanisms of the EPD system in response to three types of antibiotics and provides a scientific basis for its application in environments with fluctuating antibiotic stress.},
}

@article {pmid42096819,
year = {2026},
author = {Kumar, K and Dutta, P},
title = {Integration of mass spectrometry and molecular biotechnology to study bioaerosols.},
journal = {Chemosphere},
volume = {405},
number = {},
pages = {144949},
doi = {10.1016/j.chemosphere.2026.144949},
pmid = {42096819},
issn = {1879-1298},
abstract = {Conventional culture-based and microscopic approaches yield limited information about the diversity, content, and real-time behaviour of biological aerosols. In recent years, mass spectrometry (MS) and molecular biotechnology have evolved as powerful and complementary analytical methods for detecting, identifying, and characterising air biological particles. This study critically reviews recent improvements in MS-based techniques for analysing bioaerosol chemical markers, proteins, metabolites, and toxins, including MALDI-TOF MS, GC-MS, LC-MS/MS, and real-time aerosol mass spectrometry. In parallel, contemporary advances in molecular biotechnology, including as PCR-based assays, metagenomics, and MS-driven proteomics and metabolomics, are described, with a focus on atmospheric applications. Special emphasis is placed on integrated analytical workflows that combine MS with molecular techniques to improve specificity, sensitivity, and source attribution. The current issues of low biomass concentrations, sampling artefacts, data interpretation, and standardisation are discussed, and future perspectives on portable MS systems, multi-omics integration, and AI-assisted data processing are presented. This study offers a thorough analytical chemistry viewpoint on next-generation methodologies for monitoring bioaerosols and promotes the development of enhanced instruments for assessing air quality and protecting human health.},
}

@article {pmid42097292,
year = {2026},
author = {Hennecart, B and Belda, E and de Lahondès, R and Zucker, JD and Prifti, E},
title = {StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag212},
pmid = {42097292},
issn = {1367-4811},
abstract = {SUMMARY: Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda.

RESULTS: Applied to the CAMI II strain-madness dataset, StrainMake   produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity.

StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi : 10.5281/zenodo.16950162).},
}

@article {pmid42097342,
year = {2026},
author = {Yin, D and Chen, M and Chen, X and Feng, Y and Zhou, X and Guan, Y and Zhang, Y and Bai, S and Li, L and Ouyang, H and Cheng, J and Zhu, W},
title = {Integrative multi-omics reveals that Pueraria thomsonii Radix alleviates dyslipidemia by remodeling gut microbiota and regulating arachidonic acid metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121816},
doi = {10.1016/j.jep.2026.121816},
pmid = {42097342},
issn = {1872-7573},
abstract = {Pueraria thomsonii Radix (PTR, "Fen-ge") is a food-medicine herb widely used in China for metabolic complaints. Its putative lipid-modulating effects are supported by traditional practice, but the molecular basis remains incompletely understood.

AIM OF THE STUDY: To elucidate the active constituents and mechanisms by which PTR mitigates dyslipidemia.

MATERIALS AND METHODS: Chemical profiling and plasma exposure of PTR constituents were characterized by UPLC-Q-TOF-MS/MS. A high-fat-diet rat model was used to assess pharmacodynamic endpoints including serum lipid panel, hepatic histopathology, liver injury markers and inflammatory cytokines. Untargeted plasma metabolomics was performed in rats and patients; rat fecal 16S rRNA gene sequencing and hepatic transcriptomics complemented mechanism inference. Multivariate models were cross-validated and FDR-controlled; pathway and multi-omics correlation analyses integrated metabolite-microbe-gene relationships.

RESULTS: PTR significantly ameliorated dyslipidemia in high-fat diet-fed rats, as evidenced by improved serum lipid profiles, reduced ALT/AST levels, and alleviated hepatic steatosis and inflammation in histopathological examination. Integrated metabolomic analysis across rats and patients revealed that the restored metabolic pathways were primarily concentrated in arachidonic acid and unsaturated fatty acid metabolism. Gut microbiota analysis indicated that PTR remodeled microbial taxa correlated with arachidonic acid-related lipid metabolism. Meanwhile, hepatic transcriptomics data showed that differentially expressed genes were functionally enriched in biological processes such as lipid oxidation and were bioinformatically linked to the AMPK signaling pathway.

CONCLUSIONS: PTR may ameliorate dyslipidemia through coordinated modulation of the gut microbiota and arachidonic acid metabolic network. Based on integrated omics analysis, the hepatic AMPK signaling pathway may potentially be involved in this regulatory process; however, its direct mechanistic role requires further experimental validation. Future investigations employing targeted lipid-omics, protein phosphorylation assays, and microbiota-transfer experiments are warranted to elucidate the causal relationships.},
}

@article {pmid42097354,
year = {2026},
author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S},
title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2026.04.005},
pmid = {42097354},
issn = {2666-335X},
abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

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

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

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

@article {pmid42097759,
year = {2026},
author = {Li, Z and Zhang, Q and Wang, H and Zhang, Z and Liu, J and Li, L and Lin, Y and Wang, Y and Yin, C and Wang, W and Shen, F and Han, Z and Hao, S and Cong, P and Tian, T and Liu, Q and Chen, X and Zhan, H and Peng, T and Yu, X and Pu, X and Lian, X and Wang, T},
title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Suspected Native Spinal Brucella Infection: A Multicenter Study.},
journal = {Neurospine},
volume = {23},
number = {2},
pages = {487-499},
doi = {10.14245/ns.2551698.849},
pmid = {42097759},
issn = {2586-6583},
support = {2023YFC2812004//National Key Research and Development Program/ ; 24-4-4-zrjj-154-jch//Qingdao Natural Science Foundation/ ; //Qingdao City Healthcare Key Discipline Construction Project/ ; 2023TSGC051l//Technological Innovation Capability Improvement Project/ ; ZR2024MH251//Shandong Provincial Natural Science Foundation General Project/ ; 202404070869//Shandong Province Medical and Health Science Project/ ; },
abstract = {OBJECTIVE: The aim is to study the diagnostic positive rates of metagenomic next-generation sequencing (mNGS), microbial culture, and serologic testing in suspected native spinal brucellosis, and to evaluate the clinical value of their combined application.

METHODS: In this multicenter, retrospective observational study, 128 patients with suspected native spinal brucellosis from 6 medical centers (February 2020 to February 2025) were enrolled. Specimens from infection sites were subjected to microbial culture, mNGS, and serological testing (agglutination test).

RESULTS: Of the 128 patients with suspected native spinal Brucella infections, 118 patients were diagnosed with Brucella spondylitis. Among the 118 confirmed Brucella spondylitis cases, mNGS demonstrated a positivity rate of 92.37% (109 of 118), significantly higher than that of culture (26.27%, 31 of 118) and agglutination test (83.05%, 98 of 118). In the 87 culture-negative samples, mNGS detected Brucella in 91.95% (80 of 87), compared to 82.76% (72 of 87) by agglutination test. mNGS confirmed Brucella infection in all 16 cases that were agglutination test negative. mNGS combined with agglutination tests can effectively complement each other, improving the sensitivity of diagnosis and thereby minimizing missed diagnoses to the greatest extent. Among the 10 nonbrucellar spinal pathologies, agglutination test showed a high false-positive rate of 90% (9 of 10), whereas mNGS had a 10% (1 of 10) false-positive rate. Therefore, the agglutination test has a relatively high rate of false positives.

CONCLUSION: mNGS detection represents an effective adjunct to microbial culture and the agglutination test. The concurrent use of all 3 methods enhances diagnostic accuracy and reduces the likelihood of missed and incorrect diagnoses, significantly improving patient prognosis and guiding personalized clinical treatment.},
}

@article {pmid42098163,
year = {2026},
author = {Weng, Y and He, S and Luo, Z and Sun, J and Cheng, Q and Chen, Y and Tong, H},
title = {Keystone microbial taxa in the formation of stale aroma during pile fermentation of ripened Pu-erh tea.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00794-8},
pmid = {42098163},
issn = {2396-8370},
support = {CYB23127//Chongqing Graduate Student Research Innovation Project/ ; 2024J1110//Yunnan Provincial Department of Education/ ; 32272764//National Natural Science Foundation of China/ ; },
abstract = {Ripened Pu-erh tea is prized for its distinctive stale aroma. Methoxy-phenolic compounds, key contributors to this aroma, are produced during pile fermentation; however, the specific microorganisms responsible for their synthesis remain unclear. In this study, we identified the dominant taxa (Aspergillus luchuensis, A. fumigatus, Staphylococcus gallinarum, and S. kloosii) during pile fermentation through morphological analysis and metagenomic profiling. Gas Chromatography-Mass Spectrometry (GC-MS) analysis demonstrated the pivotal role of methoxy-phenolic compounds in the stale aroma. Moreover, using a metagenomic-based Weighted Gene Co-expression Network Analysis (WGCNA) combined with bivariate correlation network analysis, we identified key microbial taxa (Trichomonascus ciferrii, Heyndrickxia coagulans and Enterococcus sp.) involved in the generation of these compounds. Finally, we found that solid-state fermentation involving both dominant and keystone microbial taxa produced the highest levels of methoxy-phenolic compounds. Our findings reveal an inconsistency between dominant high-abundance taxa and keystone microbial taxa responsible for methoxy-phenolic compound synthesis during pile fermentation.},
}

@article {pmid42098310,
year = {2026},
author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C},
title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10221-z},
pmid = {42098310},
issn = {2399-3642},
support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.},
}

@article {pmid42098386,
year = {2026},
author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y},
title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10162-7},
pmid = {42098386},
issn = {2399-3642},
support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.},
}

@article {pmid42098439,
year = {2026},
author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ},
title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01627-1},
pmid = {42098439},
issn = {2730-664X},
abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.

METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.

RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.

CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.},
}

@article {pmid42098757,
year = {2026},
author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J},
title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42098757},
issn = {1674-9782},
support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; },
abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

RESULTS: Fifty‑six lactating Holstein cows (28 high‑yield cows, HY; 28 low‑yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high‑yield control (HCON), high‑yield SIF (HSIF), low‑yield control (LCON), and low‑yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.},
}

@article {pmid42098796,
year = {2026},
author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V},
title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02420-x},
pmid = {42098796},
issn = {2049-2618},
support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; },
abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.},
}

@article {pmid42086823,
year = {2026},
author = {Ismaeil, M and Saeed, AM and Donia, SA and El-Sayed, WS},
title = {Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42086823},
issn = {2045-2322},
mesh = {*Hot Springs/microbiology ; *Sulfur/metabolism ; *RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Soil Microbiology ; Hot Temperature ; Proteobacteria/genetics/metabolism ; },
abstract = {Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.},
}

*Hot Springs/microbiology
*Sulfur/metabolism
*RNA, Ribosomal, 16S/genetics
Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Soil Microbiology
Hot Temperature
Proteobacteria/genetics/metabolism

@article {pmid42087721,
year = {2026},
author = {Pan, W and Tang, S and Wanek, W and Luo, Z and Chen, J and Yang, Y and Ge, T and Marsden, KA and Liang, G and Chadwick, DR and Chen, X and Gregory, AS and Wu, L and Liang, Y and Jones, DL and Ma, Q},
title = {Microbial Community Traits and Necromass Dynamics Shape Soil Carbon Accumulation.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70906},
doi = {10.1111/gcb.70906},
pmid = {42087721},
issn = {1365-2486},
support = {U24A20575//National Natural Science Foundation of China/ ; 32573140//National Natural Science Foundation of China/ ; 32402680//National Natural Science Foundation of China/ ; 2024M752818//China Postdoctoral Science Foundation/ ; 2026SNJF084//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 2025SNJF025//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 202303AC100013//Yunnan Key Research and Development Program/ ; 05//Smart Fertilization Project/ ; BBS/E/RH/23NB0007//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; //Lawes Agricultural Trust/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; Fertilizers/analysis ; *Microbiota ; *Carbon Sequestration ; },
abstract = {Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long-term response to fertilisation remains unclear. Using the 180-year Broadbalk Experiment (the world's longest-running fertilisation trial; Rothamsted, UK), combined with [14]C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource-limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no-fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy-intensive enzyme synthesis. This metabolic efficiency facilitated a dual-pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg[-1], while microbial assimilation and necromass accumulation concurrently increased mineral-associated organic carbon (MAOC) from 6.8 to 21.5 g kg[-1]. Conversely, inorganic fertilisation induced an oligotrophic 'mining' strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon-limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta-analysis of field experiments (0-120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time-dependent manner, reaching a 77% gain after 80 years (three-fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long-term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism/analysis
Fertilizers/analysis
*Microbiota
*Carbon Sequestration

@article {pmid42088021,
year = {2026},
author = {Wang, A and Wang, Q and Zhang, T and Qi, G and Ren, W and Tian, W and Chen, J},
title = {Integrated multi-omics profiling reveals phenotype- and tissue-specific host-microbiota interactions in paired tumor and peritumoral tissues of advanced gastric cancer patients from Northwest China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1763765},
pmid = {42088021},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; China ; Female ; Male ; Middle Aged ; Gene Expression Profiling ; Gastric Mucosa/microbiology/pathology ; Aged ; Phenotype ; *Host Microbial Interactions/genetics ; Metagenomics ; *Microbiota ; Transcriptome ; Adult ; Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Multiomics ; },
abstract = {BACKGROUND: Advanced gastric cancer (AGC) exhibits a high incidence in Northwest China, largely attributed to region-specific dietary patterns and environmental exposures. Its pathogenesis involves complex host-microbiota crosstalk, which has not yet been comprehensively elucidated through integrated multi-omics approaches. Herein, we employed trasncriptomic and shotgun metagenomic sequencing on paired tumoral and peritumoal mucosal tissues from 88 AGC patients in Northwest China. Our aim was to systematically characterize host gene expression profiles, the composition and functional potential of the gastric mucosal microbiota, and their intricate interrelationships.

RESULTS: Transcriptomic profiling clearly distinguished tumoral from peritumoral regions (PERMANOVA, R[2] = 0.24, P = 0.0001), with 8870 differentially expressed genes (DEGs) identified between the two tissue types. Tumor tissues harbored 8377 up-regulated DEG, which were enriched in extracellular matrix (ECM) organization, cell cycle regulation, signaling transduction, and inflammatory pathways (e.g., PI3K-Akt, IL-17 signaling). In contrast, peritumoral tissues showed 493 up-regulated DEGs primarily associated with metabolic processes. Host gene expression was significantly modulated by Lauren classification in tumoral mucosa (P = 0.025) and by Helicobacter pylori (Hp) infection in peritumoral tissues (P = 0.0424). Hp-infected tissues exhibited 65 up-regulated DEGs linked to transcriptional misregulation in cancer, inflammation, immune activation and mitochondrial pathways. Lauren subtypes displayed distinct transcriptomic signatures: intestinal-type AGC was enriched in metabolic processes, diffuse-type in immune and signal transduction pathways, and mixed-type in Ras/MAPK/ErbB and NF-κB signaling pathways. Correlation analysis between the 8870 DEGs and seven differentially abundant bacterial species (e.g., Serratia surfactantfaciens, Pseudomonas protegens, Prevotella jejuni, and Streptococcus infantis) revealed 13199 significant correlations. Among these, S. surfactantfaciens and P. protegens exhibited the strongest connectivity with host genes. Functionally, the correlated DEGs were involved in ECM structure, cell cycle progression, immune and inflammatory responses, cellular proliferation and differentiation, and metabolic processes.

CONCLUSIONS: Our findings demonstrated phenotype- and tissue-specific regulation of host gene expression in AGC and revealed extensive host-microbe interactions. This work fills a critical gap in multi-omics research on AGC in the Northwest Chinese population and suggests potential diagnostic and therapeutic targets for AGC.},
}

Humans
*Stomach Neoplasms/microbiology/pathology/genetics
China
Female
Male
Middle Aged
Gene Expression Profiling
Gastric Mucosa/microbiology/pathology
Aged
Phenotype
*Host Microbial Interactions/genetics
Metagenomics
*Microbiota
Transcriptome
Adult
Helicobacter Infections/microbiology
*Gastrointestinal Microbiome
Helicobacter pylori
Multiomics

@article {pmid42088457,
year = {2026},
author = {Li, P and Kahsen, J and Olsson-Francis, K and Green, SJ},
title = {Using Carrier DNA in Ultra-Low Input Library Preparations for Next-Generation Sequencing.},
journal = {Journal of biomolecular techniques : JBT},
volume = {37},
number = {1},
pages = {18-26},
pmid = {42088457},
issn = {1943-4731},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Gene Library ; *DNA/genetics ; Polymerase Chain Reaction/methods ; *Metagenomics/methods ; Metagenome/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The purpose of this study was to evaluate the use of carrier DNA (i.e., exogenous DNA spike-in) for shotgun metagenome sequencing of ultra-low levels (less than 50 picograms) of metagenomic DNA. The study hypothesized that carrier DNA would improve the robustness of library preparation for samples with DNA concentrations that are below detection by providing a tangible amount of known DNA thereby bringing total DNA concentrations closer to recommended input ranges for metagenomic library kits. The study employed adaptive polymerase chain reaction (PCR) cycling using an iconPCR instrument (N6tec) to allow dynamic thermocycling until a sufficient library for sequencing was amplified, regardless of the input DNA concentration. Libraries were sequenced and mapped in order to reference genomes of Lambda and mock community organisms, and outcome measures included total reads, on-target reads, evenness of coverage across 10 organisms within each mock community, and PCR duplication rate. The study demonstrated that libraries can be prepared down to 50 fg of input DNA, but there is a strong correlation between input DNA concentration and PCR duplication rate. The utility of spiking in carrier DNA is equivocal as it has mild negative impacts on the observed distribution of mock communities and serves as a loss of sequencing output. Although the loss of sequencing capacity due to carrier DNA can be partially offset by a reduced loss of data from PCR duplication, carrier DNA spike-in is not recommended for routine library preparation of ultra-low input samples. Adaptive cycling allows for appropriate cycling conditions when input DNA concentrations are below detection.},
}

*High-Throughput Nucleotide Sequencing/methods
*Gene Library
*DNA/genetics
Polymerase Chain Reaction/methods
*Metagenomics/methods
Metagenome/genetics
Sequence Analysis, DNA/methods

@article {pmid42089121,
year = {2026},
author = {Bhagat, S and Kushwaha, S and Singh, S},
title = {Targeted Gut Delivery of Zn, Cu, and Mn Nanominerals Alleviates Oxidative Stress by Activating Endogenous SOD Enzymes.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e71209},
doi = {10.1002/adhm.71209},
pmid = {42089121},
issn = {2192-2659},
support = {C0046//National Institute of Animal Biotechnology, Hyderabad/ ; },
abstract = {Trace minerals such as Zn, Cu, and Mn are essential for maintaining cellular redox balance as cofactors of key antioxidant enzymes, including SOD1 and SOD2. However, their oral supplementation is often limited by poor stability in the acidic gastric environment and low intestinal absorption. Here, we report the synthesis of methionine-coated-ZnO (Met-ZnO), ascorbic acid-coated Cu2O (AA-Cu2O), and dextran-coated MnO2 (Dex-MnO2) nanominerals, followed by encapsulation into pH-responsive microcapsules (NMs-MCap) for targeted intestinal delivery. The nanomineral mixture demonstrated strong antioxidant activity at physiological pH by scavenging superoxide radicals, hydrogen peroxide, and ABTS[•+] radicals. In intestinal epithelial (IEC-6) cells, nanominerals significantly alleviated BSO-induced oxidative stress, reducing apoptosis, necrosis, and intracellular ROS accumulation. Oral administration of NMs-MCap in Zn, Cu, and Mn-deficient rats elevated mineral levels in blood and liver, mitigated BSO-induced oxidative damage, reduced lipid peroxidation and pro-inflammatory cytokines, and preserved tissue architecture. Importantly, oral supplementation restored SOD1 and SOD2 expression in key organs, supporting enhanced endogenous antioxidant defense. Metagenomic analysis revealed that mineral deficiency, combined with oxidative stress, caused gut dysbiosis, reducing beneficial taxa and enriching opportunistic ones. Nanomineral supplementation restored microbial balance, increased SCFA-producing bacteria, and improved antioxidant and metal-handling functions, establishing NMs-MCap as a safe, targeted antioxidant strategy supporting host health.},
}

@article {pmid42089290,
year = {2026},
author = {Banday, MM and Banday, S and Rahman, M and Harrison, AO and Singh, N and Moore, RM and Khan, MM and Shankar, S and Goda, Y and Coppolino, A and Movval, N and Stutts, S and Woolley, A and Dishaw, L and Goldberg, H and Mebratu, Y and Polson, SW and Patel, KN and Gaggar, A and Hayes, D and Krishnamoorthy, N and Gewurz, BE and Washko, G and Tesfaigzi, Y and Rehman, R and Sharma, NS},
title = {Anellovirus-Mediated Interferon Dysregulation Enhances Virus-Induced Lung Injury.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrcmb/aanag048},
pmid = {42089290},
issn = {1535-4989},
abstract = {BACKGROUND: The lung virome (LV) and its interactions with the host-immune system leading to allograft injury after lung transplantation are not well characterized.

METHODS: Shotgun metagenomics and qPCR was performed on a multicenter BAL/serum cohort from lung transplant recipients (LTRs). Viral constructs from betatorquevirus clade and group 2 TTVs were transfected in primary bronchial epithelial cells (PBECs) or airways of C57BL/6 mice with and without exposure to Influenza A (IAV) or RSV.

RESULTS: LV in LTRs was dominated by viruses from the family Anelloviridae. CLAD LV was characterized by the enrichment of betatorquevirus clade (BTV). Validation in an independent cohort confirmed BTV abundance in CLAD BAL, serum and lung tissues. BTV ORF1 protein (kV1) suppressed PBEC IFNα and IFNγ responses by preventing intranuclear STAT translocation. Co-culture of IAV or RSV in kV1 transfected PBECs significantly augmented replication of RSV and IAV and increased cellular injury. Likewise, in-vivo transfection of kV1 increased replication and lung injury associated with IAV.

CONCLUSION: Our work illuminates a novel virus-associated dysregulation of host interferon responses that promote lung injury associated with respiratory viral infections and, in part, explain differential host responses to viral infections after lung transplantation.},
}

@article {pmid42089622,
year = {2026},
author = {Mustajab, M and Basler, N and De Smet, L and de Graaf, DC and Matthijnssens, J},
title = {Coding-complete genome sequence of a divergent black queen cell virus strain identified from honeybees (Apis mellifera) in Romania.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0012226},
doi = {10.1128/mra.00122-26},
pmid = {42089622},
issn = {2576-098X},
abstract = {We report the 8,451-nt coding-complete genome sequence of a divergent black queen cell virus strain (BQCV-Ro). This strain was identified via retrospective analyses of metagenomic virome data of Apis mellifera samples from Europe. The genome assembly is supported by extensive read mapping, with 100% horizontal coverage and a mean sequencing depth of ~338,171×. and shares 94.3% identity with the BQCV Yeongdeok isolate.},
}

@article {pmid42090957,
year = {2026},
author = {Kämpfer, P and Lipski, A and Lawrence, KS and Olive, WR and Newman, MM and McInroy, JA and Viver, T},
title = {Pseudomonas corni sp. nov., Pseudomonas oplopanacis sp. nov., Pseudomonas salicis sp. nov., Pseudomonas rosaeacicularis sp. nov., Pseudomonas artemisiae sp. nov., Pseudomonas imperatae sp. nov. and Zestomonas ipomoeae sp. nov., isolated from rhizospheres showing plant growth promoting potential.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126719},
doi = {10.1016/j.syapm.2026.126719},
pmid = {42090957},
issn = {1618-0984},
abstract = {Several bacterial strains affiliated with the genera Pseudomonas and Zestomonas were isolated from rhizosphere samples and screened for plant growth-promoting (PGP) traits. Nine strains were analyzed polyphasically, showing ANI and dDDH values below or near species thresholds, together with phenotypic and biochemical traits supporting their differentiation. Genomic analyses revealed a repertoire of PGP-associated functions, including vitamin and cofactor biosynthesis (riboflavin, cobalamin, and thiamin), and high-affinity nutrient acquisition systems as phosphate transporters and phosphonate utilization. All strains encoded traits relevant to the rhizosphere inferred from genome annotation, including genes involved in auxin and cytokinin biosynthesis, oxidative stress tolerance, dissimilatory nitrate reduction, sulfur assimilation, and siderophore production. Metagenomic screening showed that most species are globally distributed across plant-associated, soil, freshwater, and animal-associated habitats. Based on phylogenetic, genomic, and phenotypic evidence, the strains represent seven novel species: Pseudomonas rosaeacicularis sp. nov., with AK-381[T] as the type strain (= LMG 34445[T] = CCM 9596[T]); Pseudomonas corni sp. nov., with AK-10[T] as the type strain (= CCM 9599[T] = LMG 34325[T]); Pseudomonas oplopanacis sp. nov., with AK-188[T] as the type strain (= CCM 9593[T] = LMG 34326[T]); Pseudomonas salicis sp. nov., with AK-309[T] as the type strain (= CCM 9595[T] = LMG 34328[T]); Pseudomonas artemisiae sp. nov., with DT-100[T] as the type strain (= LMG 32880[T] = DSM 115114[T] = CCM 9281[T]); Pseudomonas imperatae sp. nov., with ST-212[T] as the type strain (CCM 9594[T] = LMG 34330[T]); and Zestomonas ipomoeae sp. nov., with ST-55[T] as the type strain (LMG 32881[T] = CCM 9283[T] = DSM 115239[T]).},
}

@article {pmid42082982,
year = {2026},
author = {Li, J and Guo, S and Yu, H and Hong, X and Nie, J and Sun, H},
title = {Thyroid functional state-dependent dysbiosis of gut microbiota in Hashimoto's thyroiditis: a cross-sectional metagenomic profiling study.},
journal = {Thyroid research},
volume = {19},
number = {1},
pages = {},
pmid = {42082982},
issn = {1756-6614},
abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is a prevalent autoimmune thyroid disease (AITD) closely linked to genetic predisposition and environmental factors. Gut microbiota dysbiosis has recently been implicated as a critical contributor to AITDs' pathogenesis. Our study aims to systematically investigate the dynamic alterations in gut microbial communities under varying thyroid functional statuses and elucidate their underlying mechanisms.

METHODS: 67 HT patients with varying thyroid functional statuses and 23 healthy controls were enrolled. Fecal 16 S rDNA sequencing and analyses (alpha diversity, LEfSe, correlation, functional pathways) assessed microbiota-thyroid function links.

RESULTS: HT patients with hypo/hyperthyroidism had lower gut microbiota richness than euthyroid patients (more reduced in hyperthyroidism). The hyperthyroid group exhibited enrichment of Fusobacterium, the hypothyroid group was dominated by Clostridium sensu stricto_1, and the euthyroid group showed a predominance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Lactobacillus). Clostridium sensu stricto_1 positively correlated with TPO-Ab levels but negatively correlated with FT3.Pro-inflammatory genera(e.g., Escherichia-Shigella, Streptococcus) demonstrated negative correlations with FT3.Functional prediction analysis revealed potential associations with L-tyrosine degradation in the hyperthyroid group, reduced proportions of bile acid metabolism pathways in the hypothyroid group, and enriched proportions of fatty acid metabolism pathways in the euthyroid group.

CONCLUSIONS: This study revealed that gut microbiota dysbiosis is closely associated with thyroid functional statuses in HT. Specific bacterial genera, such as Clostridium sensu stricto_1 and Fusobacterium, may contribute to immune regulation and disease progression. The dynamic alterations in gut microbial profiles provide potential biomarkers for precision diagnosis and treatment of HT.},
}

@article {pmid42083021,
year = {2026},
author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S},
title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00898-4},
pmid = {42083021},
issn = {2524-6372},
support = {2022YFD1500600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.

RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.

CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.},
}

@article {pmid42083059,
year = {2026},
author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B},
title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02419-4},
pmid = {42083059},
issn = {2049-2618},
support = {284894//Fonds de recherche du Québec/ ; },
abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.

RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade ≥ 2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade ≥ 2 irAE had a lower alpha diversity compared to those who did not develop grade ≥ 2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade ≥ 2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin immunofluorescence signal and increased TNF-α and IL-1β expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also maintained after treatment with P. bifermentans < 3 kDa filtered supernatant.

CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.},
}

@article {pmid42083116,
year = {2026},
author = {Onohuean, FE and Onohuean, M and Olot, H and Onohuean, H},
title = {Poor Glycemic Control in East Africa: Prevalence, Risk Factors and Public Health Implications in Diabetes Management.},
journal = {Endocrinology, diabetes & metabolism},
volume = {9},
number = {3},
pages = {e70233},
doi = {10.1002/edm2.70233},
pmid = {42083116},
issn = {2398-9238},
mesh = {Humans ; *Glycemic Control/statistics & numerical data ; Africa, Eastern/epidemiology ; Risk Factors ; Prevalence ; *Public Health ; *Diabetes Mellitus/epidemiology/therapy/blood ; Cross-Sectional Studies ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; *Diabetes Mellitus, Type 2/epidemiology/blood/therapy ; },
abstract = {BACKGROUND: Diabetes mellitus remains a major public health concern in East Africa, and poor glycaemic control continues to drive avoidable complications, deaths and pressure on already stretched health systems.

OBJECTIVE: To estimate the prevalence of poor glycemic control and describe the main factors associated with it among people living with diabetes in East Africa.

METHODS: This review synthesized evidence from observational studies, cross-sectional surveys and regional health databases identified through PubMed, Scopus and Web of Science, following PRISMA guidance. Sociodemographic, clinical and behavioural indicators were examined to identify common patterns and predictors of poor glycaemic control. The review also considered how measurement approaches shaped reported estimates.

RESULTS: Fifty records were identified across PubMed (10), Scopus (23) and Web of Science (17). After screening, 37 records were eligible for full-text review, and 15 studies met the inclusion criteria for evidence synthesis. Across the region, poor glycemic control was consistently high, ranging from 60% to 85%. Most studies were facility-based and cross-sectional. Glycemic control was assessed mainly using HbA1c, commonly defined as ≥ 7% or > 7.5%, and less frequently by fasting blood glucose, typically ≥ 7.2 mmol/L or > 130 mg/dL. Type 2 diabetes was the dominant population studied, with fewer mixed cohorts and only one study focused on type 1 diabetes. Factors repeatedly linked to poor control included older age, longer duration of diabetes, poor medication adherence, limited access to care, low health literacy, inadequate diabetes education, insulin use, comorbidities, diabetic complications, unhealthy diet, physical inactivity, sedentary behaviour, substance use and limited self-management support.

CONCLUSION: Poor glycemic control is alarmingly common among people with diabetes in East Africa and reflects intertwined clinical, behavioural and health-system challenges. Region-specific strategies are needed to strengthen primary care, improve diabetes education, expand affordable monitoring and treatment and enhance surveillance to guide policy and resource allocation.},
}

Humans
*Glycemic Control/statistics & numerical data
Africa, Eastern/epidemiology
Risk Factors
Prevalence
*Public Health
*Diabetes Mellitus/epidemiology/therapy/blood
Cross-Sectional Studies
Blood Glucose/analysis
Glycated Hemoglobin/analysis
*Diabetes Mellitus, Type 2/epidemiology/blood/therapy

@article {pmid42083299,
year = {2026},
author = {Qin, R and Wang, C and Cong, M and Tian, L and Li, N},
title = {Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.},
journal = {Cancer medicine},
volume = {15},
number = {5},
pages = {e71915},
doi = {10.1002/cam4.71915},
pmid = {42083299},
issn = {2045-7634},
support = {JYKY2024-0050409022//Beijing Vlove Charity Foundation/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Neoplasms/complications ; Aged ; *Pneumonia/diagnosis/microbiology ; Sputum/microbiology ; Adult ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: With the development of new sequencing technologies, metagenomic next-generation sequencing (mNGS) has become a diagnostic tool for respiratory tract infections. Patients with cancer may develop pneumonia caused by infections or antitumor therapy. Therefore, pneumonia in patients with cancer is more complex than that in healthy individuals. Currently, few reports are available on the use of mNGS for diagnosing pneumonia in patients with cancer.

METHODS: In this retrospective study, 14 patients with cancer diagnosed with pneumonia in March 2023 were enrolled from the Emergency Department of the Chinese Academy of Medical Sciences Cancer Hospital. Sputum samples from the patients were examined using conventional tests and mNGS to identify pathogens. The mNGS and conventional test results were compared to assess the diagnostic yield in patients with cancer.

RESULTS: The overall pathogen detection rate of mNGS was 64.29% (9/14), with corresponding diagnostic sensitivity, specificity, false-negative rate and false-positive rate of 90.00%, 25.00%, 10.00% and 75.00%, respectively. Among 13 paired sputum specimens, mNGS exhibited a numerically higher pathogen detection rate (61.54%, 8/13) than conventional diagnostic assays (38.46%, 5/13). McNemar's paired chi-square test demonstrated no statistically significant difference between the two detection methods (p = 0.37), and Kappa concordance analysis generated a coefficient of 0.27 (p = 0.23), suggesting poor inter-method consistency. Compared with conventional tests, mNGS detected additional pathogens in 8 specimens and identified a greater number of pathogens in 9/14 (64%) samples. Moreover, mNGS results led to diagnostic revisions and subsequent antimicrobial therapy adjustments in 64% (9/14) of enrolled patients. Additionally, mNGS detected antibiotic resistance genes in five patients, which provided guidance for antibiotic selection.

CONCLUSIONS: Metagenomic next-generation sequencing (mNGS) showed potential value in pathogen detection, as it appeared to identify pathogens more rapidly and comprehensively than conventional methods. It may provide auxiliary support for the diagnosis and treatment of pneumonia in this vulnerable population.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
*Metagenomics/methods
Retrospective Studies
*Neoplasms/complications
Aged
*Pneumonia/diagnosis/microbiology
Sputum/microbiology
Adult
Sensitivity and Specificity

@article {pmid42083599,
year = {2026},
author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV},
title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.},
journal = {Acta naturae},
volume = {18},
number = {1},
pages = {55-63},
pmid = {42083599},
issn = {2075-8251},
abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.},
}

@article {pmid42084116,
year = {2026},
author = {Qi, J and Liang, C and Zhang, C and Wang, M and Wei, G and Jiao, S},
title = {Intensifying Aridity Undermines the Role of Soil Biodiversity in Supporting Ecosystem Stability.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70903},
doi = {10.1111/gcb.70903},
pmid = {42084116},
issn = {1365-2486},
support = {42477129//National Science Foundation of China/ ; JYB2025XDXM706//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Biodiversity ; *Soil Microbiology ; *Climate Change ; China ; *Soil/chemistry ; *Ecosystem ; *Desert Climate ; },
abstract = {Biodiversity is widely recognized for enhancing ecosystem stability, yet its contribution is highly sensitive to climate change. However, whether and how climatic factors, particularly aridity, modulate the role of soil biodiversity in stabilizing ecosystems remains poorly understood. Here, we integrated a comprehensive soil survey of 265 dryland agricultural fields along a 3800 km east-west transect in China with a global meta-dataset encompassing 996 sites across six continents. Our analysis revealed a positive association between soil biodiversity and ecosystem stability, quantified using 11-year Normalized Difference Vegetation Index (NDVI) data (2012-2022). Critically, both our field data and global synthesis revealed that increasing aridity significantly weakened this biodiversity-stability relationship. The decline in soil microbial network complexity with increasing aridity partially explains this decoupling. Metagenomic analyses further showed that as aridity increased, microbial life history strategies shifted toward greater investment in stress tolerance at the expense of growth yield and resource acquisition. Together, our findings represent a substantial advance in revealing how intensifying aridity undermines the role of soil biodiversity in supporting ecosystem stability, and highlight the importance of microbial network complexity and life history strategies as key predictors of biodiversity-stability relationships under global change.},
}

*Biodiversity
*Soil Microbiology
*Climate Change
China
*Soil/chemistry
*Ecosystem
*Desert Climate

@article {pmid42084385,
year = {2026},
author = {Rodríguez, P and Simon, SA and Probst, AJ and Magnabosco, C},
title = {Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150025},
doi = {10.1128/msystems.01500-25},
pmid = {42084385},
issn = {2379-5077},
abstract = {Cosmopolitan microbial lineages are found in anoxic sediments worldwide, but the details about their ecology and evolution remain underexplored. In this study, we identified persistent populations from these cosmopolitan lineages belonging to Planctomycetes, Chloroflexi Atribacteria, and Candidatus Bathyarchaeia from an ~8,000-year sedimentary sequence. To investigate the genomic variations within these persistent populations, a pangenome of each population was constructed using all non-redundant metagenome-assembled genomes (MAGs) recovered from the sedimentary sequence and was screened for enriched functional genes, single-nucleotide polymorphism (SNP) density, dN/DS ratios, and pseudogene content. Our results show that the majority of persistent populations studied possess large variable genomes enriched for energy conservation and transcriptional regulation functions with increasing depth, whereas Planctomycetes retain a highly conserved, SNP-poor core genome. Analysis of SNPs across depths indicates progressive isolation with burial, while a subset of core genes shows signatures of positive selection. Collectively, the data support depth-associated selection acting alongside drift across Lake Cadagno's persistent sedimentary lineages.IMPORTANCEThroughout the subsurface, multiple examples of "evolutionary stasis" have been reported in microbial lineages that exhibit lower rates of metabolic activity and cellular turnover. This study uses an ~8,000-year sedimentary record of Lake Cadagno to evaluate how persistent populations of cosmopolitan bacteria and archaea have changed with burial and identifies signals of progressive genetic isolation along with positive selection of population-specific subsets of core genes with depth. Together, these changes show that Lake Cadagno's persistent populations are not in stasis but diverge over time and burial.},
}

@article {pmid42084478,
year = {2026},
author = {Wang, C and Dou, P and Wang, Y and Li, X and Zhang, Y and Ma, X},
title = {A wolf in sheep's clothing: An unusual zoonotic pathogen in peritoneal dialysis effluent and an important diagnostic strategy.},
journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis},
volume = {},
number = {},
pages = {8968608261448060},
doi = {10.1177/08968608261448060},
pmid = {42084478},
issn = {1718-4304},
abstract = {Brucellosis is an infectious disease characterized by a natural foci, caused by Brucella, a genus of Gram-negative bacilli known for its obligate aerobic growth and capability for intracellular parasitism. This pathogen can be transmitted zoonotically between animals and humans. Due to its mechanism of intracellular survival, monotherapy with a single antibiotic often proves ineffective in eradicating Brucella. Therefore, clinical management necessitates the implementation of multidrug combination therapy alongside extended therapeutic regimens to achieve optimal bacteriological clearance. Conventional diagnostic methods, such as bacterial culture and serological testing, are frequently hindered by the fastidious growth requirements of the pathogen and the risk of false-positive serological cross-reactivity. These limitations may result in delayed diagnosis or unnecessary interventions. Recent advancements in molecular biology-particularly genomic analysis technologies-have revolutionized pathogen detection by facilitating rapid and precise identification of elusive pathogens. This study reports the first documented case of refractory peritoneal dialysis-associated peritonitis caused by Brucella diagnosed via metagenomic next-generation sequencing (mNGS). By employing mNGS to identify the pathogen, we summarize the clinical characteristics of this case and highlight the diagnostic advantages of this technology. Our findings aim to guide clinicians in selecting appropriate diagnostic approaches for similar cases, avoiding unnecessary delays and optimizing resource utilization in clinical practice.},
}

@article {pmid42084497,
year = {2026},
author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD},
title = {Characterizing microbiomes of African fermented foods in a global context.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001695},
pmid = {42084497},
issn = {1465-2080},
mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Food Microbiology ; Metagenome ; Fermentation ; Africa ; Kenya ; Burkina Faso ; Ghana ; },
abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.},
}

*Fermented Foods/microbiology
*Microbiota/genetics
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
*Food Microbiology
Metagenome
Fermentation
Africa
Kenya
Burkina Faso
Ghana

@article {pmid42084683,
year = {2026},
author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M},
title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42084683},
issn = {1614-7499},
abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.},
}

@article {pmid42084764,
year = {2026},
author = {Joshi, G and Khannam, KS},
title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42084764},
issn = {1432-072X},
mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.},
}

*Microbiota
*Biotechnology
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Biodegradation, Environmental

@article {pmid42085791,
year = {2026},
author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D},
title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142255},
doi = {10.1016/j.jhazmat.2026.142255},
pmid = {42085791},
issn = {1873-3336},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.},
}

@article {pmid42085838,
year = {2026},
author = {ElHefnawi, M and Amin, DH and Elfiky, AM and Tamam, FMM and Elabiad, MA and Zada, S and Abu-Shahba, N},
title = {From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117449},
doi = {10.1016/j.diagmicrobio.2026.117449},
pmid = {42085838},
issn = {1879-0070},
abstract = {Infective endocarditis (IE) is a severe disease that damages heart valves and can lead to major complications, including heart failure, embolic events, and stroke. It is the third most common fatal infection worldwide. This review examines the clinical burden of IE, its microbial causes, and the ongoing challenges in diagnosis. Particular attention is given to the limitations of traditional blood cultures, especially in detecting culture-negative and fastidious organisms, and to the emerging role of metagenomic approaches. A comprehensive review of the literature was conducted, focusing on diagnostic methods such as blood cultures, molecular assays, and metagenomic sequencing. The role of bacterial biofilms in treatment failure and antibiotic resistance was also explored. Metagenomics, especially cell-free metagenomic DNA (cf-mDNA), shows promise as a non-invasive diagnostic tool that can overcome culture-based limitations. However, standardized protocols and prospective studies are needed to validate its routine clinical application in IE diagnosis and management.},
}

@article {pmid42085875,
year = {2026},
author = {Amin, H and Šantl-Temkiv, T and M Wouters, I and Johannesen, A and Sigsgaard, T and Schlünssen, V and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ},
title = {Urban indoor airborne antibiotic resistance genes: Role of antibiotic use and outdoor air pollution.},
journal = {The Science of the total environment},
volume = {1034},
number = {},
pages = {181854},
doi = {10.1016/j.scitotenv.2026.181854},
pmid = {42085875},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) in airborne dust represent an emerging concern for public health, particularly in indoor environments where human exposure is prolonged. While external environmental pressures are known to shape the abundance and diversity of microorganisms in indoor dust, their role in ARG dynamics remains underexplored. This study assessed the temporal and spatial patterns of airborne ARGs in indoor dust across four Nordic cities (Aarhus, Bergen, Reykjavik, and Uppsala) using electrostatic dust collectors (EDCs) in the same households at two time points: 2012 and 2022. Shotgun metagenomic sequencing was performed to profile ARGs. National antibiotic consumption data were obtained from the European Surveillance of Antimicrobial Consumption (ESAC-Net), outdoor air pollution data (PM2.5 and PM10) from the Copernicus Atmosphere Monitoring Service (CAMS), and meteorological parameters from the NASA POWER database. Beta diversity analysis revealed city-specific differences in ARG composition (PERMANOVA, R[2] = 0.18, P = 0.03), but no consistent temporal shift over the 10-year period. Macrolide, tetracycline, and aminoglycoside resistance genes were among the most abundant and persistent classes. A previously undetected macrolide resistance sequence was identified across all cities in 2022. Although national antibiotic consumption declined, cross-sectional correlations between national antibiotic consumption and ARG abundance strengthened from 2012 (Spearman's ρ = 0.25) to 2022 (ρ = 0.37), suggesting sustained ARG presence despite reduced antibiotic consumption. Several ARG classes showed associations with outdoor particulate matter, and these relationships were influenced by local meteorological conditions. For example, higher absolute humidity was associated with a weaker relationship between PM and polymyxin resistance genes, whereas stronger wind speeds were associated with stronger relationships between PM and Sulfonamide resistance genes. These findings highlight the complex environmental interplay between antibiotic consumption, air pollution, meteorological factors, and ARG dynamics in indoor air, emphasizing the need for integrated environmental and AMR surveillance, especially in the context of climate change.},
}

@article {pmid42085931,
year = {2026},
author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB},
title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.},
journal = {EBioMedicine},
volume = {127},
number = {},
pages = {106281},
doi = {10.1016/j.ebiom.2026.106281},
pmid = {42085931},
issn = {2352-3964},
abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.

METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).

FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.

INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.

FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).},
}

@article {pmid42086548,
year = {2026},
author = {Lu, M and Jiao, JJ and Luo, X and Feng, X and Liang, W and Yu, S and Qi, Y and Wang, Z and Li, H and Li, M},
title = {Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72058-8},
pmid = {42086548},
issn = {2041-1723},
support = {32225003, 32393970, 32393971, 92251306//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407109//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42130702//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Elevated ammonium concentrations in deltaic groundwater pose a widespread environmental challenge, yet the microbial mechanisms linking depositional history to ammonium dynamics remain poorly understood. The Pearl River Delta, with the highest naturally occurring groundwater ammonium concentrations documented globally, provides a unique natural system to investigate these processes. Here, by integrating geochemical and metagenomic data, we show that fermentation-related genes are the most prevalent across all depositional zones, suggesting fermentation as the potential primary pathway for ammonium production, with the functional potential declining as sedimentary organic matter becomes increasingly recalcitrant with sediment age. Secondary mechanisms shift from nitrate reduction to nitrite ammonification across terrestrial-to-marine-dominated zones, reflecting salinity-driven metabolic partitioning. Notably, the marine-derived genus Brevirhabdus emerges as a key taxon linking depositional history to present-day biogeochemistry, demonstrating remarkable metabolic versatility. These findings demonstrate that paleo-depositional and hydrogeological evolution fundamentally shape microbial landscapes and dictate groundwater quality in deltaic systems worldwide.},
}

@article {pmid42086631,
year = {2026},
author = {Moon, K and Kang, I and Cho, JC},
title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07383-0},
pmid = {42086631},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; },
abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.},
}

@article {pmid42071227,
year = {2026},
author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z},
title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.},
journal = {Clinical and translational medicine},
volume = {16},
number = {5},
pages = {e70667},
doi = {10.1002/ctm2.70667},
pmid = {42071227},
issn = {2001-1326},
support = {2022YFA1304000//National Key R&D Program of China/ ; 2024B1111150001//Guangdong S&T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; },
abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.},
}

*Colorectal Neoplasms/microbiology/genetics/pathology/etiology
Humans
Animals
*DNA Damage/drug effects
Mice
Male
*Lactates/metabolism/adverse effects
Gastrointestinal Microbiome
*Carcinogenesis
Female
Feces/microbiology
Middle Aged

@article {pmid42071909,
year = {2026},
author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R},
title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/ani16081137},
pmid = {42071909},
issn = {2076-2615},
support = {NA//Alltech (Ireland)/ ; },
abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.},
}

@article {pmid42072313,
year = {2026},
author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S},
title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040772},
pmid = {42072313},
issn = {2227-9059},
support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; },
abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.},
}