@article {pmid41729089,
year = {2026},
author = {Liu, J and Zheng, X and Jia, C and Sun, Z and Zhou, W and Zhang, J and Chen, Y and Zhou, Z and Tian, Y and Xiao, G and Du, L and Fan, C and Sun, L and Yue, M},
title = {Zoonotic Bordetella bronchiseptica Infection at the Swine-Human Interface: Unveiling the Evolutionary Path from an Animal to a Human Pathogen.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2637286},
doi = {10.1080/22221751.2026.2637286},
pmid = {41729089},
issn = {2222-1751},
abstract = {Bordetella bronchiseptica, long regarded as a veterinary pathogen, is now emerging as a zoonotic threat to humans, particularly in immunocompromised individuals. We report a sentinel event involving a synchronized B. bronchiseptica outbreak in swine and their human caretaker, providing a unique opportunity to examine cross-species transmission and adaptation at the genomic level. Comparative genomics revealed that the human-adapted isolate (RL57) and its swine progenitor (XX35) share an identical chromosome, with XX35 harboring an extra conjugative plasmid. Remarkably, RL57 did not simply lose this plasmid; instead, the entire plasmid was integrated into the chromosome via site-specific recombination. This integration allowed permanent retention of plasmid-encoded virulence and fitness genes, after which the plasmid was discarded to eliminate its replicative burden-a "capture-and-discard" mechanism of evolution. Following plasmid loss, the RL57 strain exhibited hypervirulence, faster growth, enhanced thermotolerance, and increased biofilm formation, indicating successful adaptation to the human host. Plasmid loss paradoxically rewired bacterial metabolism: sulfur assimilation and sulfonate utilization pathways were upregulated to fuel host adaptation. Strikingly, despite a collapse in transcription of specific metabolic modules, translational compensation maintained high protein levels, driving robust biofilm formation and thermal tolerance. These findings reveal a previously unrecognized evolutionary strategy in which plasmid integration followed by subsequent plasmid loss amplifies pathogenicity and host adaptability. Finally, we propose a One Health surveillance triad-metagenomic tracking of plasmid-chromosome dynamics, recombination hotspot screening, and metabolic shift monitoring-to proactively identify and mitigate such zoonotic events.},
}

@article {pmid41729067,
year = {2026},
author = {Liu, Y and Zhang, T and Liu, J and Dong, X},
title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14510},
pmid = {41729067},
issn = {1520-5118},
abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.},
}

@article {pmid41728996,
year = {2026},
author = {Li, Z and Zhang, H and Wei, T and He, L and Wang, Y},
title = {Anoxia-adapted cyanobacteria in a marine blue hole.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0257625},
doi = {10.1128/aem.02576-25},
pmid = {41728996},
issn = {1098-5336},
abstract = {Vertical transmission of marine particles brings ocean surface cyanobacteria into the deep ocean, where heterotrophic cyanobacterial lineages probably evolve to adapt to new environments even in oxygen-depleted zones. At present, active cyanobacteria have rarely been reported in dark and anoxic water columns in the deep sea. In this study, we recovered three metagenome-assembled genomes of cyanobacteria from the Yongle blue hole located in the South China Sea, two of which were actively transcribed in a dark, anoxic environment at 250 m depth, through integrated metagenomic and metatranscriptomic analyses of water samples from 21 stratified depths collected using in situ microbial fixation and filtration. These anoxia-adapted cyanobacteria were phylogenetically approximate to the sponge cyanobacterial symbionts, while the genomic features showed similarities with both free-living and sponge symbiotic counterparts. They exhibit genomic features shared with symbiotic lineages, including loss of substrate utilization, biosynthesis pathways, DNA repair, and circadian regulation. Conversely, they retain selected metabolic characteristics of free-living lineages, including phenylalanine biosynthesis and phosphoserine metabolism. Additionally, the discovery of taurine transport proteins in the genomes suggests the potential for organic sulfur uptake from the environment. Altogether, these findings reveal a distinct genomic configuration in cyanobacteria inhabiting a permanently dark and anoxic marine system, characterized by the retention of oxygen-dependent metabolic potential alongside sustained transcriptional suppression under in situ conditions. This study provides new insights into the ecological persistence and evolutionary adaptation of cyanobacteria under long-term oxygen limitation.IMPORTANCEWe report metabolically active cyanobacteria thriving in darkness and oxygen deprivation at 250 m depth in the ocean. Genomics results show these microbes share evolutionary roots with sponge cyanobacterial symbionts but developed unique adaptations for anoxic and sulfidic environments. Strikingly, they retain photosynthesis genes as genomic remnants (with no detected transcription) while losing genes critical for environmental stress responses, including DNA repair, osmotic regulation, and circadian control, suggesting a potential evolutionary connection to symbiotic relatives. Crucially, they maintain metabolic autonomy via phenylalanine biosynthesis and light-independent serine biosynthesis, exhibiting traits absent in most symbionts. This demonstrates how cyanobacteria adapt to anoxic environments through targeted genome reduction, revealing novel survival strategies in oxygen-depleted oceans and providing a research case for microbial resilience during marine deoxygenation.},
}

@article {pmid41728976,
year = {2026},
author = {La, N and Rattanapitoon, NK and Thanchonnang, C and Rattanapitoon, SK},
title = {Beyond a viral succession timeline: a phase-transition framework and re-analysis highlight hidden instability in the proposed "phage clock".},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0230725},
doi = {10.1128/aem.02307-25},
pmid = {41728976},
issn = {1098-5336},
}

@article {pmid41728963,
year = {2026},
author = {Enuh, BM and Myers, KS and Ackman, P and Weiland, T and Beach, N and Young, M and Donohue, TJ and Noguera, DR},
title = {Metagenomes and metagenome-assembled genomes from a nutrient removal plant at Los Angeles County Sanitation Districts (LACSD) that transitioned from high to low dissolved oxygen.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0149425},
doi = {10.1128/mra.01494-25},
pmid = {41728963},
issn = {2576-098X},
abstract = {Operating biological nutrient removal (BNR) wastewater treatment plants with low dissolved oxygen (DO) conditions can reduce energy costs. We report on five metagenomes and 492 metagenome-assembled genomes (MAGs) obtained from samples collected at the Pomona water reclamation plant before and after a DO reduction from 3.5 to 0.7 mg/L.},
}

@article {pmid41728322,
year = {2026},
author = {Kim, DD and Worby, CJ and Wharton, H and Miklos, A and Chieng, B and Njenga, SM and Earl, AM and Pickering, AJ},
title = {Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.08.26345864},
pmid = {41728322},
abstract = {Bacterial infections are a major cause of morbidity and mortality among children under five in low- and middle-income countries (LMICs). Children in LMICs are exposed to and colonized by a range of pathogenic bacteria, yet patterns of bacterial exchange between humans are not well known, in part because culturing and sequencing single bacterial isolates is labor-intensive. Here, we apply a machine learning strain tracking approach to metagenomic data from 511 stool samples from children and mothers across urban and rural Kenyan communities to characterize bacterial dissemination and assess if community-wide water chlorination disrupts transmission. We identified distinct strain-sharing dynamics across species; potentially pathogenic taxa (e.g., Escherichia , Enterococcus , Campylobacter) exhibited distance-dependent dissemination driven by young children, while commensal taxa (e.g., Bifidobacterium , Bacteroides) showed patterns consistent with dietary exposure. Drinking water chlorination reduced community-level strain-sharing in rural communities. Our study provides the first strain-level insights into multi-species bacterial transmission dynamics in LMIC communities, identifying distinct dissemination pathways for facultative versus mostly anaerobic bacteria. Moreover, our findings highlight the utility of metagenomic strain tracking to uncover how community spread can be disrupted.},
}

@article {pmid41728114,
year = {2026},
author = {Jiang, YL and Dong, SZ and Xu, YB and Fan, JL and Zhang, YM and Huang, SS},
title = {Metagenomic next-generation sequencing for diagnosis of immune checkpoint inhibitor-associated pneumonitis: a retrospective comparative clinical performance study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1730022},
pmid = {41728114},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; *Pneumonia/diagnosis/chemically induced/microbiology/etiology ; Sensitivity and Specificity ; Neoplasms/drug therapy ; Aged, 80 and over ; Immunotherapy/adverse effects ; },
abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in distinguishing immune checkpoint inhibitor-related pneumonitis (CIP) from infectious pneumonia in cancer patients undergoing immunotherapy.

METHODS: A retrospective tertiary hospital cohort included 34 cancer patients (Feb 2022-Jan 2024) with prior ICI exposure, new/worsening respiratory symptoms, imaging infiltrates, and both mNGS and conventional microbiological testing (CMT). Final diagnoses were adjudicated by a multidisciplinary panel. We compared pathogen detection rates, sensitivity, specificity, and turnaround times (TAT) between mNGS and CMT.

RESULTS: In the infectious pneumonia group, mNGS detected pathogens in 17/18 cases (94%), whereas CMT detected only 6/18 (33%). In the CIP group, mNGS was negative in 14/16 cases (88%), compared with 11/16 negatives by CMT (69%). Using the adjudicated diagnosis as the reference, mNGS showed sensitivity 88%, and specificity 94%. In contrast, CMT's sensitivity was 69%, and specificity 33%. The median TAT for mNGS was 24 hours (IQR 22-31 h), versus 121.5 hours (IQR 80.5-156 h) for CMT (P < 0.001).

CONCLUSION: mNGS outperforms CMT in both diagnostic accuracy and timeliness for distinguishing CIP from infectious pneumonia among immunotherapy recipients. Incorporation of mNGS into the diagnostic workflow for suspected CIP may improve etiological discrimination and enable timely, individualized treatment. Further large-scale prospective studies are required to confirm these findings.},
}

Humans
Retrospective Studies
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
*Metagenomics/methods
Aged
*Pneumonia/diagnosis/chemically induced/microbiology/etiology
Sensitivity and Specificity
Neoplasms/drug therapy
Aged, 80 and over
Immunotherapy/adverse effects

@article {pmid41726958,
year = {2026},
author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.12.705600},
pmid = {41726958},
issn = {2692-8205},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid41726932,
year = {2026},
author = {Montes, A and Klopmanbaerselman, D and Lee, B and Quiñones, B and Shim, H},
title = {Temporal dynamics of microbiome communities within urban compost piles undergoing the heat process.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.10.705224},
pmid = {41726932},
issn = {2692-8205},
abstract = {Urban composting supports soil health but also intersects with food safety, where compost is produced near farms and communities. Here, we profiled temporal microbiome dynamics across a 6-week heat compost cycle from the urban compost piles using paired physicochemical panels and long-read metagenomics. Nutrient composition and pH shifted with compost age, coinciding with stage-structured microbial succession, including temperature-linked turnover of compost communities from mesophilic to thermotolerant taxa. Bacterial profiles included the presence of antimicrobial resistance genes and foodborne-associated genera early in the cycle, with reduced representation during the thermophilic phase. Analysis of previously unclassified long reads reveals an extensive repertoire of putative bacteriophages, including several complete genomes and candidates linked to foodborne bacteria, and their abundance is coupled to the host abundance. Together, these results support thermophilic composting as a key mitigation step for microbiological hazards in urban-adjacent systems and identify compost piles as a promising reservoir for discovering candidate lytic phages for downstream isolation and host-range testing.},
}

@article {pmid41726920,
year = {2026},
author = {Jensen, JSL and Maharjan, S and Münch, PC and Shen, J and Bowcutt, B and Sumner, JT and Morgan, XC and Thompson, KN and Nguyen, LH and Franzosa, EA and Huttenhower, C},
title = {Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.11.705346},
pmid = {41726920},
issn = {2692-8205},
abstract = {Viruses are crucial components of microbial communities, both phage that infect bacterial community members as well as pathogenic and other eukaryotic viruses. However, they remain unobserved by most current technologies, due to combinations of experimental and analytical factors. To address the latter, we developed the BAQLaVa algorithm for high-resolution profiling of >120,000 viral species (viral genome bins, VGBs) via reference-based metagenome (MGX) or metatranscriptome (MTX) alignment to complementary nucleotide markers and proteome sets. In comprehensive benchmarking, BAQLaVa substantially outperformed alternatives, achieving species-level recall and precision regularly over 90%. We applied BAQLaVa to MGX and MTX samples from the HMP2 IBDMDB cohort to identify previously undescribed viral perturbations in inflammatory bowel diseases. Most notably, virome diversity was reduced in tandem with bacterial diversity during inflammation, in contrast to previous findings based on a narrower range of viral detection. A subset of viruses were enriched during IBD, associated with carriage of abortive infection anti-defense systems such as AbiL and PD-λ-2, as well as genes involved in the regulation of lysogeny. Leveraging the corresponding viral profiles, we also inferred phage-host relationships using scalable co-occurrence and covariation signals, even in the absence of host references or genome annotations. By enabling high sensitivity and specificity viral profiling from metagenomes or metatranscriptomes, BAQLaVa provides a scalable framework for virome epidemiology and systematic analysis of virus-host interactions.},
}

@article {pmid41726864,
year = {2026},
author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A},
title = {Metagenomic surveillance of undiagnosed febrile illness in Nigeria does not reveal the etiological agent for most patients.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.07.704564},
pmid = {41726864},
issn = {2692-8205},
abstract = {Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false negative and false positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and Chikungunya. Here, we show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76 %) in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.},
}

@article {pmid41726584,
year = {2026},
author = {Xie, G and Zhou, Q and Liao, J and Zheng, Y and Wang, W and Shen, K},
title = {The ketogenic diet alters microbiome-metabolome profiles to improve West syndrome therapy.},
journal = {Pediatric investigation},
volume = {10},
number = {1},
pages = {10-24},
pmid = {41726584},
issn = {2574-2272},
abstract = {IMPORTANCE: The ketogenic diet (KD) is effective in managing epilepsy, particularly West syndrome (WS); however, the role of gut microbiome (GM) and metabolome in its efficacy remains unclear. Understanding these mechanisms could optimize the KD for WS treatment.

OBJECTIVE: To identify microbiome-metabolome signatures associated with KD efficacy in WS by analyzing changes in GM composition and metabolic pathways.

METHODS: Fecal samples were collected from WS patients (n = 16) and healthy children (n = 24). Metagenome and metabolome analyses were performed to assess GM composition and metabolic profiles.

RESULTS: WS patients showed GM imbalances compared to healthy children. Disease status contributed sufficiently to the GM. The abundance of Bacteroides, Parabacteroides, and Faecalibacterium was lower in WS (3.30% vs. 39.86%, P-adj = 0.140; 0.14% vs. 0.73%, P-adj = 0.023; 0.04% vs. 1.35%, P-adj = 0.018), whereas Bifidobacterium and Escherichia were higher (6.08% vs. 2.23%, P-adj = 0.140; 7.57% vs. 0.15%, P-adj < 0.001). After KD, Parabacteroides (particularly P. distasonis) and Bacteroides (particularly B. fragilis) increased (0.14% vs. 0.35%, P-adj = 0.034; 3.30% vs. 21.18%, P-adj = 0.380); Bifidobacterium (particularly B. breve) and Escherichia (particularly E. coli) decreased from 6.08% and 7.57% to 1.24% and 2.52%, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that ATP-binding cassette (ABC) transporters, fatty acid biosynthesis, tyrosine metabolism, and other pathways were significantly altered in patients with WS, and these alterations were reversed following ketogenic diet (KD) consumption. The KD also altered intestinal metabolites. Integrative analysis of microbial features, gene functions, and metabolites revealed that Bacteroides species and P. distasonis were significantly associated with ABC transporters, alanine aspartate and glutamate metabolism, and negatively correlated with 3-sulfinoalanine, suggesting potential regulatory roles in metabolic pathways.

INTERPRETATION: KD induces significant shifts in GM composition and metabolic pathways, which may contribute to its therapeutic efficacy in WS. The restoration of Bacteroides and Parabacteroides dominance, alongside alterations in gene functions and neurotransmitter-related metabolites, suggests a potential mechanism for the antiepileptic effects of KD.},
}

@article {pmid41726388,
year = {2025},
author = {Donbraye, E and McLeod, L and Carson, CN and Chai, Z and Lacoste, SR and Herman, EK and McCarthy, EL and Hill, JE and Erickson, NEN and Pollock, C and Links, MG and Otto, SJG and Gow, S and Stothard, P and Campbell, JR and Waldner, CL},
title = {Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1704412},
pmid = {41726388},
issn = {2297-1769},
abstract = {INTRODUCTION: Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs).

METHODS: Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing.

RESULTS: Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples (p < 0.05). Bovine viral diarrhea virus 1 (BVDV-1) and 2 (BVDV-2) were rarely detected at either time. The most prevalent viruses detected in YRL arrival samples were BRBV (42%), BRSV (39%), BPIV-3 (20%), IDV (16%), BCoV (12%), and BVDV-2 (7.5%). The prevalences of BRSV (60%), BPIV-3 (39%), and BVDV-2 (17%) were higher in 14 DOF samples than arrival samples (p < 0.05). BRSV (OR 7.0, 1.7-29) and BPIV-3 (OR 5.7, 1.5-21) were more likely to be detected in arrival samples from YRL than FPC (p = 0.01). In 14 DOF samples, BPIV-3 (OR 4.9, 1.3-19, p = 0.02) and BVDV-2 (OR 13, 2.0-83, p = 0.01) were identified more frequently in YRL than FPC. These data allowed the identification of respiratory bacteria and 33 ARGs in parallel with assessment of the viral components. The most prevalent bacteria detected in FPC at arrival were Mannheimia haemolytica (35%), Histophilus somni (35%) and Pasteurella multocida (23%). Detection of M. haemolytica increased at 14 DOF (p = 0.02), while P. multocida detection decreased (p = 0.03). At both arrival and 14 DOF in YRL, M. haemolytica was the most prevalent bacterium, followed by P. multocida and H. somni with no significant differences between arrival and 14 DOF samples. ARGs were detected more frequently in the 14 DOF samples than at arrival for both FPC (p = 0.03) and YRL (p = 0.01). The most commonly detected ARGs were associated with resistance to lincosamides and aminoglycosides; however, ARGs associated with other antimicrobials used in cattle including tetracyclines were also identified.

DISCUSSION: Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.},
}

@article {pmid41726216,
year = {2026},
author = {Gui, J and Long, C and Fu, Y and He, H and Li, J and Wang, F},
title = {Performance Evaluation of Targeted Nanopore Sequencing in Non-Tuberculous Mycobacteria Identification: A Comparative Study in Shenzhen, China.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {572430},
pmid = {41726216},
issn = {1178-6973},
abstract = {OBJECTIVE: This study aims to analyze the performance differences between targeted nanopore sequencing, Sanger sequencing, and metagenomic sequencing in comparatively identifying non-tuberculous mycobacteria (NTM) species. Additionally, it explores the clinical application potential of targeted nanopore sequencing for identifying NTM clinical isolates in the Shenzhen region.

METHODS: This retrospective study collected a total of 50 suspected NTM isolates from drug-resistant tuberculosis surveillance across 10 districts in Shenzhen, China, between December 2024 and June 2025. The species of the NTM isolates were initially identified using fluorescence PCR probe melting curve analysis. Genomic DNA was extracted from all 50 isolates, and species identification was performed using targeted nanopore sequencing (tNS), metagenomic sequencing (mNGS), and Sanger sequencing. The Jaccard similarity index, Kappa coefficient for classification consistency, and F1 score for model performance were calculated to evaluate the concordance among the three sequencing methods and assess the detection performance of targeted nanopore sequencing in NTM species identification.

RESULTS: The most frequently detected NTM species by tNS, mNGS, and Sanger sequencing were M.abscessus and M.fortuitum, while M. tuberculosis was predominantly identified through mNGS results. Among the 50 suspected NTM samples, 18 (36%) showed complete concordance between tNS, mNGS, and Sanger sequencing, with the highest agreement observed between mNGS and tNS (28 samples, 56%). The final species identification reference results for the 50 samples were confirmed through a comprehensive evaluation using the Jaccard similarity coefficient, precision, and recall. Based on reference results, the F1 scores for tNS, mNGS, and Sanger sequencing were 0.927, 0.896, and 0.543, respectively. The tNS exhibited the highest concordance with the reference results, outperforming the other two methods.

CONCLUSION: tNS represents a preferred auxiliary methodology for clinical identification of NTM isolates in Shenzhen, China, with identification results optimally validated through integration with mNGS findings. This study provides strong support for the application of tNS technology for NTM species identification.},
}

@article {pmid41725821,
year = {2026},
author = {Wang, C and Zhang, C and Shah, AM and Wang, Z and Qiu, S and Xu, Z and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Peng, Q},
title = {The optimal dietary crude protein level improves goat production performance by enhancing the body's antioxidant function and energy metabolism.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1734810},
pmid = {41725821},
issn = {1664-302X},
abstract = {The current research was conducted to evaluate the impact of various crude protein (CP) concentrations in diets on growth performance, nutrient digestibility, nitrogen deposition, rumen fermentation, microbial community, and serum metabolomics in growing goats. Fifty healthy 4-month-old Chuannan black goats (Capra hircus) with similar body weight (13.75 ± 0.27 kg) were randomly distributed into 5 groups. Goats were fed diets with five different levels of CP: 8.12% (T8), 10.15% (T10), 12.17% (T12), 14.13% (T14), and 16.18% (T16), respectively. The total duration of the trial was 70 d, including a 14-day adaptation period. The average daily gain and feed conversion ratio displayed a quadratic upsurge and reduce respectively, with the rise of CP content in the diet. The group T14 exhibited the highest average daily gain and demonstrated the best feed conversion efficiency. A linearly (p < 0.05) increase of the digestibility of dry matter, neutral detergent fiber, and acid detergent fiber was observed, whereas a quadratic effect (p < 0.001) on nitrogen intake, fecal nitrogen, and urinary nitrogen was obtained with the increase of dietary CP. Moreover, dietary CP levels had a quadratic effect on the concentration of ruminal ammonia nitrogen (p = 0.021), rumen microbial protein (p = 0.042), total volatile fatty acid (p = 0.012), acetate (p = 0.040), isobutyrate (p = 0.024), and isovalerate (p < 0.001). Microbial metagenomics results showed that the relative abundance of Burkholderia and Bacillus increased (p < 0.05), while the relative abundance of Pseudomonas and Salmonella decreased (p < 0.05) when comparing group T14 to group T8. Metabolomic results showed that differently expressed metabolites were found to enrich the proline, glutathione and arginine metabolism, and citric acid cycle metabolic pathway. The concentration of serum genistein was positively correlated (p < 0.05, r = 0.665) with the abundance of Bacillus and negatively correlated (p < 0.05, r = -0.734) with the abundance of Pseudomonas. It is concluded that a dietary CP level of 14% enhances the antioxidant function and energy metabolism of the goats by altering the composition of rumen microorganisms, thereby improving production performance.},
}

@article {pmid41725015,
year = {2026},
author = {Wang, R and Wang, Z and Liao, W and Wang, T and Su, Y},
title = {Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02334-8},
pmid = {41725015},
issn = {2049-2618},
support = {31872670//National Natural Science Foundation of China/ ; 2021A1515010911//Guangdong Basic and Applied Basic Research Foundation/ ; 202206010107//Science and Technology Projects in Guangzhou/ ; JCYJ20210324141000001//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; },
abstract = {BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses.

RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation.

CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.},
}

@article {pmid41725012,
year = {2026},
author = {Ramírez, AL and Páez, L and Vega, L and Aya, V and Hernández, C and Luna, N and Muñoz, M and Patiño, LH and Ramírez, JD},
title = {Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {41725012},
issn = {1757-4749},
abstract = {BACKGROUND: The human gut virome is a fundamental yet understudied component of the intestinal microbiome. However, its taxonomic composition and functional potential in Latin American populations remain poorly understood, particularly under clinical stressors such as hospitalization and diarrhea conditions often linked to microbial dysbiosis.

METHODS: We conducted a hybrid metagenomic analysis of the human gut virome from 37 fecal samples: 10 from patients admitted to intensive care units (ICU), 13 from hospitalized patients outside the ICU (Non-ICU), and 14 from non-diarrheic individuals, including taxonomic and functional profiling of viruses and detection of viral auxiliary metabolic genes (vAMGs).

RESULTS: We identified 494 high-quality viral vOTUs, from which 37,619 ORFs were predicted. Taxonomically, Caudoviricetes and Intestiviridae were consistently present across all groups, supporting their role as part of a conserved core virome. Functionally, we identified 309 putative vAMGs spanning 90 functional categories, primarily related to metabolism and environmental information processing. Non-diarrheic individuals harbored a higher number and diversity of vAMGs compared to hospitalized groups (Kruskal-Wallis, p < 0.01), whereas ICU and Non-ICU patients showed reduced and more variable functional profiles. Beta diversity analysis revealed that diarrhea status, rather than hospitalization per se, was associated with modest but significant shifts in functional composition (PERMANOVA, R² = 0.047, p = 0.025), driven by quantitative changes in shared AMGs rather than the presence of unique functions. Notably, resistance-related vAMGs, including bacitracin transporters and Zinc D-Ala-D-Ala carboxypeptidase, were detected across samples, highlighting the potential of phages as mobile reservoirs of antibiotic resistance.

CONCLUSION: Together, our findings indicate that hospitalization and diarrhea do not markedly alter the taxonomic structure of the gut virome but are associated with modest shifts in viral functional potential. The maintenance of a stable viral community alongside variable AMG repertoires suggests that phages may modulate host-microbiome interactions primarily through functional fine-tuning rather than large-scale community restructuring. Our study provides evidence for the ecological resilience of the human gut virome and underscores the need to integrate viral communities into resistome research.},
}

@article {pmid41724983,
year = {2026},
author = {Yang, K and Li, J and Li, L and Fu, L and Liu, W and Jia, Z and Wang, Z and Wei, Z and Zhang, F},
title = {Soil antibiotic resistome in farmland exhibits higher diversity and horizontal transfer potential than adjacent pastureland in agro-pastoral ecotone.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00871-1},
pmid = {41724983},
issn = {2524-6372},
support = {CCPTZX2024QN03//National Center of Pratacultural Technology Innovation Special fund for innovation platform construction/ ; 42407171//National Natural Science Foundation of China/ ; 2025T180072, GZB20240311//China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: Soil antibiotic resistant genes (ARGs) and mobile genetic elements (MGEs) are associated with agricultural land-use differences. However, assessing the soil antibiotic resistome differences between farmland and pastureland is often limited due to geographically unbalanced sample collection. Leveraging a typical agro-pastoral ecotone in northern China as the study model, we compared the soil microbiome and resistome between 15 adjacent farmland and pastureland pairs using metagenomic sequencing.

RESULTS: Results showed that farmland soils harbored higher soil ARG diversity (+ 2.75%), MGE diversity (+ 1.62%) and multidrug resistance-related gene abundance (+ 19.5%) than pastureland. Among them, genes conferring multidrug resistances were dominant in farmland, mainly carried by Pseudomonadota. While, vancomycin-resistant ARGs were dominant in pastureland, mainly carried by Actinomycetota. Metagenome-assembled genomes revealed that sul2 conferring sulfonamide resistance was shared by both Pseudomonadota and Acidobacteriota in farmland together with insertion sequence ISVsa3. Structural equation model analysis integrating with soil geography, pedology and microbiome data showed microbial community and soil properties were identified as major driving factors shaping soil antibiotic resistome diversity in both land-use contexts. MGE diversity showed a clear positive effect on ARG diversity in farmland soils but a minor effect in pastureland.

CONCLUSIONS: Together, this study elucidates the shared and distinguished soil antibiotic resistome pattern between farmland and pastureland, extending our understanding of driving factors in agricultural soil ARG contamination.},
}

@article {pmid41718551,
year = {2026},
author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E},
title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630482},
pmid = {41718551},
issn = {1949-0984},
mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; MicroRNAs/metabolism/genetics ; Caco-2 Cells ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.},
}

Humans
*Extracellular Vesicles/metabolism/genetics
MicroRNAs/metabolism/genetics
Caco-2 Cells
*RNA, Bacterial/metabolism/genetics
*Epithelial Cells/microbiology/metabolism
*Gastrointestinal Microbiome

@article {pmid41724868,
year = {2026},
author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR},
title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.},
journal = {Archives of virology},
volume = {171},
number = {3},
pages = {},
pmid = {41724868},
issn = {1432-8798},
mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; *Carcinoma, Lewis Lung/complications/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Male ; },
abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.},
}

Animals
*Cachexia/virology/etiology/microbiology
*Dysbiosis/virology
*Virome
Mice
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Disease Models, Animal
*Carcinoma, Lewis Lung/complications/virology
*DNA Viruses/genetics/classification/isolation & purification
Male

@article {pmid41724800,
year = {2026},
author = {Bhuyan, B and Chutia, B and Singh, LS},
title = {Emerging strategies for heavy metal removal in soils: plant-microbe interactions and omics perspectives.},
journal = {Archives of microbiology},
volume = {208},
number = {5},
pages = {},
pmid = {41724800},
issn = {1432-072X},
mesh = {*Metals, Heavy/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Plants/microbiology/metabolism ; *Soil Microbiology ; Soil/chemistry ; Metabolomics ; Bacteria/metabolism/genetics ; Proteomics ; },
abstract = {Rapid industrial expansion, intensive agricultural practices, and widespread petroleum extraction have led to the significant buildup of heavy metals (HMs) in soils and related ecosystems, posing serious environmental and public health risks. Hence, this review highlights the major sources, ecological impacts, and toxicity of HMs in the environment. However, physical and chemical remediation methods can reduce HMs concentrations, but issues such as high operational costs, prolonged treatment durations, and poor sustainability limit their suitability for large-scale application. Thus, bioremediation methods, especially those that utilize plants and microbes, have gained increasing attention as eco-friendly and cost-effective options. Plant-microbe-based interactions play an important role, as they act synergistically to facilitate metal uptake, stabilization, transformation, and detoxification of HMs in contaminated soils. Though, it is important to understand the plant-microbe interactions, especially since most current research is about how plants and microbes can work together to clean up contaminants in their natural environments. However, achieving higher remediation performance under stress conditions depends on the selection of plant and microbial species. Therefore, this review explores the mechanisms of plant-microbe interactions along with omics technologies employed to analyze samples for understanding this interaction in HMs-contaminated soils at the metagenomics, metatranscriptomics, proteomics, and metabolomics levels in enhancing the effectiveness of remediation. This review article also highlights key factors affecting remediation efficiency and discusses limitations, challenges, and future prospects of plant-microbe interactions in HMs-contaminated soils.},
}

*Metals, Heavy/metabolism
Biodegradation, Environmental
*Soil Pollutants/metabolism
*Plants/microbiology/metabolism
*Soil Microbiology
Soil/chemistry
Metabolomics
Bacteria/metabolism/genetics
Proteomics

@article {pmid41724632,
year = {2026},
author = {You, TY and Lee, NY and Tsai, WC and Lo, CL and Chen, PT and Chen, SY and Jan, HE and Ko, WC},
title = {Etiological identification of Orientia tsutsugamushi by metagenomic next-generation sequencing in an adult with septic shock in Taiwan.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2026.02.002},
pmid = {41724632},
issn = {1995-9133},
}

@article {pmid41724403,
year = {2026},
author = {Zhang, Y and Liu, Y and Zhang, S and Li, Y and Zhao, L and Wang, Z and Wang, Q and Zhang, N and Bachert, C and Bröker, BM and Wang, X and Zhang, L and Lan, F},
title = {Staphylococcal Superantigens-specific IgE Reveals Functional Superantigen Production Beyond Staphylococcus aureus in CRSwNP.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.02.013},
pmid = {41724403},
issn = {1097-6825},
abstract = {BACKGROUND: Staphylococcal superantigen-specific immunoglobulin E (SAg-IgE) correlates with disease severity in type 2 (T2) chronic rhinosinusitis with nasal polyps (CRSwNP) patients. Although Staphylococcus aureus (S. aureus) is recognized as a primary source of SAgs, SAg-IgE is detected even in patients with culture-negative S. aureus. background OBJECTIVE: To identify the source of SAgs in SAg-IgE-positive T2 CRSwNP patients with culture-negative S. aureus.

METHODS: Metagenomic sequencing was conducted in T2 CRSwNP patients with repeatedly negative S. aureus cultures, stratified by SAg-IgE status. We screened clinical isolates for SAg genes and evaluated SAg functionality by measuring SAg-specific TCR repertoire expansion and T2 inflammatory responses in an ex vivo infection model.

RESULTS: The SAg-IgE-positive group showed significantly higher abundances of Staphylococcus epidermidis, S. aureus, Lysinibacillus xylanilyticus, and Staphylococcus capitis (S. capitis) compared to the SAg-IgE-negative group. Interestingly, in all participants where S. aureus was detected, S. capitis was also present, albeit at low abundance. Redundancy analysis demonstrated clustering of Staphylococcus genus, SAg-IgE, and IL-5, supporting a potential link between Staphylococcus genus and SAg-driven immune responses. Notably, a clinical S. capitis isolate carried SEA and SEC genes and secreted functional SAgs, which triggered the clonal expansion of SEA/SEC-specific TCRs and exacerbated the T2 inflammatory response via IL-33 induction. results CONCLUSIONS: Metagenomic sequencing reveals S. capitis, beyond S. aureus, produces functional SAg to drive T2 response in SAg-IgE-positive CRSwNP patients when conventional cultures fail to detect S. aureus. Independent of culturable bacterial load, tissue SAg-IgE positivity reliably indicates bacterial colonization and SAg exposure in CRSwNP.},
}

@article {pmid41724378,
year = {2026},
author = {Lin, YT and Graells, T and Sayols-Baixeras, S and Dekkers, KF and Schillemans, T and Baldanzi, G and Wuopio, J and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Association between the gut microbiota and estimated glomerular filtration rate in two Swedish population-based cohorts.},
journal = {Kidney international},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.kint.2026.01.021},
pmid = {41724378},
issn = {1523-1755},
abstract = {INTRODUCTION: Evidence for gut-kidney interactions in early kidney disease is limited, particularly in community-dwelling adults with largely preserved kidney function. Here, we quantified links between gut microbiota and estimated glomerular filtration rate (eGFR) in two population-based Swedish cohorts.

METHODS: Deep shotgun metagenomics profiled fecal samples from 9788 adults in the Swedish CArdioPulmonary BioImage Study (SCAPIS) discovery cohort (mean age 58 ± 4 years; 52 % women) and 2080 adults in the Malmö Offspring Study (MOS) replication cohort (mean age 40 ± 14 years; 52 % women). Linear regression related the relative abundance of 494 metagenome-assembled species to the creatinine-based eGFR (by CKD-EPI equation), adjusting for demographics, albuminuria, cardiovascular risk factors and technical variables. Species passing false discovery rate under 0.05 in SCAPIS were tested in MOS for significant concordant direction. Functional enrichment linked eGFR-associated species to gut metabolic modules and plasma metabolites; partial Spearman correlations assessed metabolite/species/eGFR relationships.

RESULTS: The alpha diversity showed a modest inverse association with eGFR across both cohorts. We identified 44 bacterial species consistently associated with eGFR in both cohorts, collectively explaining 7% of its variance. Enrichment analysis highlighted histidine and carnitine metabolism among the top three pathways involved. Their key products, trimethylamine N-oxide and imidazole propionate, were inversely related to eGFR, and a metabolite panel accounted for 51% of eGFR variation, underscoring metabolite-mediated microbial effects. Sensitivity analyses upheld these findings.

CONCLUSIONS: Gut microbial diversity and 44 reproducible species are independently linked to kidney function in community dwelling adults. Enrichment of histidine and carnitine pathways, and their circulating metabolites implicates microbial metabolism as a contributor to eGFR variability, suggesting tractable targets for early kidney protection.},
}

@article {pmid41724273,
year = {2026},
author = {Yang, X and Chen, H and Wu, T and Ji, ZY and Wang, ZW and Liu, ZL and Yang, JK and Zhao, Y and Zhou, M and Wang, XB},
title = {Neobavaisoflavone, a functional metabolite derived from valnemulin, ameliorates DSS-induced ulcerative colitis through activation of the AMPK signaling pathway.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {117841},
doi = {10.1016/j.bcp.2026.117841},
pmid = {41724273},
issn = {1873-2968},
abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by sustained mucosal inflammation, disrupted epithelial barrier function, microbial dysbiosis, and impaired intestinal homeostasis. If chronic uncontrolled inflammation persists, it may lead to the development of colorectal cancer or other severe clinical complications. Emerging evidence suggests that cellular senescence promotes inflammatory cascades, aggravating UC symptoms and implicating a pathophysiological link to disease progression. Our previous studies have demonstrated that the anti-senescence compound Valnemulin (VAL) can mitigate colonic senescence and alleviate UC symptoms. In this study, subsequent integrative metagenomic and metabolomic analyses revealed that VAL's pharmacological mechanism involves restructuring the gut microbial community composition, enhancing the colonization abundance of beneficial bacteria, and thereby promoting the production of their key metabolites, which collectively contribute to UC remission. In vitro and in vivo studies demonstrated that VAL's anti-senescence effects are mediated by Neobavaisoflavone (NBIF), a functional metabolite produced by beneficial gut bacteria. NBIF effectively activates the AMP-activated protein kinase (AMPK) pathway, significantly reducing the expression levels of senescence marker proteins p16, p53, and p21. Consequently, this mechanism ameliorates the senescent phenotype in intestinal epithelial cells and contributes to the overall improvement of colonic tissue senescence in UC pathology. Concomitantly, NBIF also reduces levels of pro-inflammatory cytokines IL-1β, TNF-α, and IL-6, thereby attenuating DSS-induced pathological damage in UC. This study not only proposes a novel anti-senescence strategy for UC treatment but also elucidates the pivotal role of the gut microbiota-metabolite-AMPK axis in regulating intestinal inflammation.},
}

@article {pmid41724250,
year = {2026},
author = {Li, Y and Kang, L and Qin, X and Fei, R and Lu, A and Qishuang, H},
title = {Dual mechanism of electrochemical regulation to reduce soil Nitrous Oxide emissions-microbial recruitment and electron transfer pathway optimization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134255},
doi = {10.1016/j.biortech.2026.134255},
pmid = {41724250},
issn = {1873-2976},
abstract = {Greenhouse gas emissions from agricultural nitrogen cycling, primarily Nitrous Oxide (N2O), are intrinsically linked to fertilizer dynamics. Conventional mitigation strategies emphasize synthetic fertilizer reduction, yet suffer from inefficiency and lack of sustainability. This study introduces an electrochemical regulation approach and, through comparative analysis of two fertilizers (ammonium sulfate vs. urea), elucidates dual mechanisms (redox modulation and microbial community engineering). Key findings: (1) 500 mV electrostimulation enriched nitrate-reducing microbiota, reducing N2O by 11.9 ± 5.9% (sulfate) and 14.2 ± 4.4% (urea) via enhanced denitrification; (2) Electrode interventions accelerated N2O-to-N2 conversion (15.8 ± 1.4% and 14.9 ± 8.9%) by optimizing redox fluxes and boosting electroautotrophic Pseudomonas spp. activity; (3) Urea exhibited delayed electroresponsiveness (6-10 h lag) due to slower amide nitrogen hydrolysis kinetics compared to sulfate; (4) Metagenomics confirmed upregulation of nitrogen metabolic genes (norC: 2.9×, nirD: 2.7×, narI: 2.6 ×) and restructured microbial networks. This study elucidates a fundamental electro-microbial mechanism that reconfigures nitrogen-transforming networks, providing a novel paradigm for managing soil biogeochemical cycles.},
}

@article {pmid41724049,
year = {2026},
author = {Wang, D and Xin, J and Lai, C and Sun, N and Yang, Y and He, Y and Duan, L and Luo, J and He, Y and Zhang, Y and Zhang, Y and Wang, H and Zeng, D and Bai, Y and Ni, X},
title = {High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119898},
doi = {10.1016/j.ecoenv.2026.119898},
pmid = {41724049},
issn = {1090-2414},
abstract = {Fluoride pollution-whether of geological or anthropogenic origin-disrupts gut microbiota-host homeostasis and compromises the intestinal barrier. We established an acute high-fluoride mouse model via intragastric NaF, integrating metagenomics, metabolomics, and molecular biological techniques to clarify the underlying mechanism of enhanced intestinal permeability caused by fluoride exposure in vivo. Mechanistically, high fluoride exposure activates the RhoA/ROCK signaling pathway, increases the level of phosphorylated myosin light chain (p-MLC), induces filamentous actin (F-actin) rearrangement, and disrupts the apical junctional complex (AJC)-characterized by downregulated expression or abnormal localization of AJC-related proteins (ZO-1, Claudin-1, β-catenin, Occludin). It also alters the morphology of intestinal epithelial cells, ultimately increasing ileal permeability. At the microbiota level, high fluoride disrupted the ileal microbiota; specifically, at the species level, Bifidobacterium sp. SO1 and Schaalia turicensis were identified as the key species with high specificity and high occupancy under fluoride exposure. Lactobacillus and Akkermansia were abnormally enriched in the intestines of mice exposed to fluoride. Metabolomic analysis revealed that high fluoride exposure enriched multiple pathways including linoleic acid metabolism and sphingolipid metabolism, altering the levels of 11 cytoskeleton-related metabolites. Correlation analysis confirmed that Bifidobacterium sp. SO1 and Schaalia turicensis were strongly correlated with damage phenotypes, pathway molecules, and metabolites, indicating that these two strains are closely associated with cytoskeleton changes and increased intestinal permeability under high fluoride exposure. Collectively, our findings reveal that gut microbiota drive fluoride-induced intestinal barrier dysfunction through the "microbiota-RhoA/ROCK-cytoskeleton" axis, highlighting a novel host-microbe interaction mechanism underlying environmental toxin-mediated gut injury.},
}

@article {pmid41723970,
year = {2026},
author = {Wang, L and Wang, J and Zhu, Q and Zhang, Q and Qian, J},
title = {Rapid diagnosis of a mixed pulmonary infection with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, and Cytomegalovirus in a Lymphoma patient using metagenomic next-generation sequencing: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117320},
doi = {10.1016/j.diagmicrobio.2026.117320},
pmid = {41723970},
issn = {1879-0070},
abstract = {Immunocompromised patients are at high risk for life-threatening polymicrobial infections, often challenging to diagnose conventionally. We report a 60-year-old male with relapsed angioimmunoblastic T-cell lymphoma, fever, and pancytopenia post-chemotherapy. Chest CT showed scattered inflammation. Bronchoalveolar lavage fluid (BALF) culture grew only Klebsiella aerogenes, but fluorescent staining revealed aseptate hyphae. Metagenomic next-generation sequencing (mNGS) of BALF identified concurrent infections with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus, and SARS-CoV-2 within 48 hours. Targeted therapy with isavuconazole, sulfamethoxazole-trimethoprim, and ganciclovir was promptly initiated. Despite therapy, the patient deteriorated due to profound immunodeficiency and was discharged palliatively. This case highlights mNGS as a rapid diagnostic tool for mixed infections, though clinical correlation remains essential.},
}

@article {pmid41723514,
year = {2026},
author = {Şapcı, AOB and Mirarab, S},
title = {krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03999-y},
pmid = {41723514},
issn = {1474-760X},
support = {1R35GM142725/NH/NIH HHS/United States ; 1R35GM142725/NH/NIH HHS/United States ; #2138259//National Science Foundation/ ; #2138259//National Science Foundation/ ; ASC150046//Advanced Cyberinfrastructure Coordination Ecosystem/ ; ASC150046//Advanced Cyberinfrastructure Coordination Ecosystem/ ; },
abstract = {Comparing each sequencing read in a sample to a reference database is a fundamental step in wide-ranging applications. Results of these comparisons can enable phylogenetic characterization. However, phylogenetic placement is currently only possible at scale for marker genes, a small fraction of the genome. We introduce krepp, an alignment-free k-mer-based method that enables placing reads from anywhere on the genome on an ultra-large reference phylogeny (e.g., 123,853 leaves). We show that krepp is scalable and computes accurate distances that approximate those using alignments, leading to accurate placements. These precise phylogenetic identifications improve our ability to compare and characterize metagenomic samples.},
}

@article {pmid41723359,
year = {2026},
author = {Wang, L and Xu, J and He, P and Hong, W and Jin, Y and Zeng, J and Liu, L and Liu, L},
title = {Refractory peritoneal dialysis-associated peritonitis caused by Mycobacterium tuberculosis identified by mNGS: a case report.},
journal = {BMC nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12882-026-04820-5},
pmid = {41723359},
issn = {1471-2369},
support = {0038481190612016//Zhuhai High-Level Talent Team Fund/ ; },
abstract = {BACKGROUND: Peritoneal dialysis-associated peritonitis (PDAP) is a common complication in patients undergoing peritoneal dialysis (PD) and may lead to technique failure or poor prognosis. Tuberculosis-related peritonitis in this setting is rare and difficult to diagnose because of nonspecific clinical manifestations and frequently negative conventional microbiological tests. Reporting such cases may help improve awareness and diagnostic strategies.

CASE PRESENTATION: We report the case of a 34-year-old woman with systemic lupus erythematosus and end-stage renal disease who was receiving maintenance peritoneal dialysis. She presented with fever, abdominal pain, and diarrhea. Repeated conventional bacterial and fungal cultures of peritoneal dialysis effluent and blood were negative, and empirical antibiotic therapy failed to achieve sustained clinical improvement. Metagenomic next-generation sequencing of the peritoneal dialysis effluent detected Mycobacterium tuberculosis, providing supportive diagnostic information. Based on the combined clinical presentation, molecular findings, and immunological testing, anti-tuberculosis therapy was initiated. The patient's symptoms gradually resolved, and peritoneal dialysis was temporarily suspended for 11 days before being successfully resumed. No recurrence of peritonitis was observed during a 6-month follow-up period.

CONCLUSIONS: This case highlights the diagnostic challenges of tuberculosis-related peritonitis in patients undergoing peritoneal dialysis. Metagenomic next-generation sequencing may serve as a useful adjunctive diagnostic tool in selected patients with persistent symptoms and repeatedly negative conventional cultures, facilitating earlier diagnosis and appropriate management.},
}

@article {pmid41723316,
year = {2026},
author = {Moreno, IJ and Bogdanov, A and Palenik, B},
title = {Common capacity for far-red light photosynthesis in a canyon thermophilic freshwater system.},
journal = {Extremophiles : life under extreme conditions},
volume = {30},
number = {1},
pages = {},
pmid = {41723316},
issn = {1433-4909},
abstract = {UNLABELLED: Photosynthetic life is based on absorbing sunlight and turning it into biologically usable energy. In many cases however, canopy-like structures and cavern-like habitats in terrestrial environments can limit the intensity and alter the spectra of light. One acclimation to use filtered light in the near infrared range, typically between 700 and 800 nm is named far-red light photoacclimation or FaRLiP as in recent studies of cyanobacteria. Here we report the common capacity for FaRLiP in the dominant cyanobacterial genera in a canyon hot spring microbial mat ecosystem. We identified FaRLiP in the genomes of cyanobacterial isolates and the metagenomes of mat samples. We show using absorption spectroscopy and HPLC that under far red-light specific isolates show an increase in far red-light absorption and the presence of Chl f. Springs in narrow canyons are a microniche where FaRLiP seems highly ecologically advantageous.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00792-026-01422-9.},
}

@article {pmid41723172,
year = {2026},
author = {Honda, T and Yu, S and Mai, D and Baumgart, L and Chan, EM and Babnigg, G and Yoshikuni, Y},
title = {CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69903-1},
pmid = {41723172},
issn = {2041-1723},
support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with cell growth, chemotaxis, plant immune suppression, biofilm formation, and stress responses, reflecting the coordinated physiological adaptation to the root environment. Additionally, we discovered that transcriptional activation of xanthine dehydrogenase and a lysozyme inhibitor is crucial for evading plant immune systems. This framework is scalable to other bacterial species and provides new opportunities for understanding rhizobacterial gene regulation in native environments.},
}

@article {pmid41723054,
year = {2026},
author = {Prideaux, L and Goire, N and Crook, S and Dreyer, L and Sherry, N and Mahony, AA},
title = {A case of Helicobacter cinaedi meningitis confirmed via metagenomics sequencing.},
journal = {Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pathol.2025.10.011},
pmid = {41723054},
issn = {1465-3931},
}

@article {pmid41722974,
year = {2026},
author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J},
title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.},
journal = {Food microbiology},
volume = {137},
number = {},
pages = {105022},
doi = {10.1016/j.fm.2025.105022},
pmid = {41722974},
issn = {1095-9998},
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Morus/microbiology/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Microbiota ; Temperature ; Hydrogen-Ion Concentration ; Ethanol/metabolism ; Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Acids/metabolism ; Lactobacillus/metabolism/genetics ; Stress, Physiological ; Multiomics ; },
abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.},
}

Fermentation
*Wine/microbiology/analysis
*Morus/microbiology/metabolism
Saccharomyces cerevisiae/metabolism/genetics
*Microbiota
Temperature
Hydrogen-Ion Concentration
Ethanol/metabolism
Metabolomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
*Acids/metabolism
Lactobacillus/metabolism/genetics
Stress, Physiological
Multiomics

@article {pmid41722709,
year = {2026},
author = {Arhin, SG and Esposito, G and Cesaro, A},
title = {Single-stage microbial conversion of fish waste into linear and branched medium-chain fatty acids.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134253},
doi = {10.1016/j.biortech.2026.134253},
pmid = {41722709},
issn = {1873-2976},
abstract = {Anaerobic fermentation of biowaste into medium‑chain fatty acids (MCFAs) offers a scalable route for resource recovery within a circular bioeconomy framework, yet production from protein‑rich substrates such as fish waste remains underexplored. This study investigated the valorization of fish waste into MCFAs via mono- and co-fermentation in a single-stage chain elongation process. By leveraging endogenous electron donors and protein ammonification, the system maintained favorable pH conditions and sustained MCFA synthesis without external chemical inputs. Mono-fermentation favored isocaproate (4-methylvaleric acid) production, reaching a peak yield of 166.9 ± 11.6 mg COD/g VS (5.8 ± 0.4 g COD/L). Co-fermentation with carbohydrate-rich food waste in equal proportions shifted selectivity toward n-caproate (214.5 ± 18.8 mg COD/g VS) and n-heptanoate (145.8 ± 27.7 mg COD/g VS), achieving a maximum total MCFA yield of 366.3 ± 53.1 mg COD/g VS (12.8 ± 1.9 g COD/L). Bioaugmentation with Saccharomyces cerevisiae triggered solventogenesis and excessive ethanol oxidation (EEO) possibly due to elevated ammonium concentrations. Although sodium 2-bromoethanesulfonate (BES) addition transiently suppressed EEO, EEO resumed as H2 production declined, suggesting that promoting lactate-driven chain elongation via co‑fermentation is a more robust strategy under ammonia stress. Metagenomic analysis revealed that isocaproate formation during mono‑fermentation was associated with Stickland‑type amino‑acid fermentation, with Sporanaerobacter acetigenes as a potential key contributor. In contrast, co‑fermentation enriched genes associated with lactate metabolism, acetyl‑CoA generation, and linear MCFA synthesis, primarily linked to Clostridia and Betaproteobacteria. These results reveal tunable routes to straight‑ and branched‑chain MCFAs from protein‑rich waste, supporting green approaches to platform chemical generation.},
}

@article {pmid41722567,
year = {2026},
author = {Thurimella, K and Wu, E and Li, C and Graham, DB and Owens, RM and Plichta, DR and Sokol, CL and Xavier, RJ and Bacallado, S},
title = {Identifying microbial protease allergens through protein language model-guided homology.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101510},
doi = {10.1016/j.cels.2025.101510},
pmid = {41722567},
issn = {2405-4720},
abstract = {Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic SPs in metagenomic data. First, we develop a model to identify the catalytic serine residue in serine hydrolases, demonstrating how pLMs capture structural information. Next, we create a deep learning framework to detect candidate SP allergens across gene catalogs, using the conserved catalytic triad to identify homologs in gut and oral sites despite low sequence identity. Our model predicts a putative SP allergen resembling V8 protease, a known trigger for protease-activated receptor 1. It also identifies a cysteine protease similar to Der f 1 from dust mites. Immunization with these proteases induced allergic responses, validating their allergenic potential experimentally. This approach uncovers candidate allergens beyond traditional methods, offering new targets for allergy research. A record of this paper's transparent peer review process is included in the supplemental information.},
}

@article {pmid41722379,
year = {2026},
author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM},
title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.},
journal = {The Science of the total environment},
volume = {1020},
number = {},
pages = {181545},
doi = {10.1016/j.scitotenv.2026.181545},
pmid = {41722379},
issn = {1879-1026},
abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.},
}

@article {pmid41721873,
year = {2026},
author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S},
title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41721873},
issn = {1573-4978},
mesh = {*Geologic Sediments/microbiology ; Metagenomics/methods ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Fungi/genetics ; Microbiota/genetics ; Bacteria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.

METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.

CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.},
}

*Geologic Sediments/microbiology
Metagenomics/methods
Biodiversity
Nitrogen/metabolism
Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Fungi/genetics
Microbiota/genetics
Bacteria/genetics
Phylogeny

@article {pmid41721729,
year = {2026},
author = {Wang, H and Zhao, Z and Lin, L and Dong, A and Deng, Y and Zhou, J and Ju, F},
title = {Candidatus dermatophostum as a novel genus of polyphosphate-accumulating organisms for high-strength wastewater treatment.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag032},
pmid = {41721729},
issn = {1751-7370},
abstract = {Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes (MAGs) from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named Candidatus Dermatophostum, which shows specific preference for high-phosphorus environments. Its representative species, Ca. Dermatophostum ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across WWTPs worldwide, underscoring both its diverse metabolic capabilities and potential engineering implications for mitigating nitrous oxide (N2O) emissions for EBPR system. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.},
}

@article {pmid41720887,
year = {2026},
author = {Clarenne, A and Suarez, LV and Muggeo, A and Meurice, J and Lecomte-Thenot, Q and Perotin, JM and Bessaci-Kabouya, K and Mulette, P and Abely, M and Gouriou, S and Dury, S and Deslée, G and Héry-Arnaud, G and Guillard, T},
title = {Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40314-y},
pmid = {41720887},
issn = {2045-2322},
support = {RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; RINNOPARI//University Hospital of Reims/ ; },
abstract = {Pulmonary involvement in cystic fibrosis (CF) includes bronchiectasis and chronic airway infection, with nearly half of the airway bacteria being anaerobes. Some anaerobic species, such as Porphyromonas catoniae, have been identified as predictive biomarkers for Pseudomonas aeruginosa colonization, with P. catoniae decreasing as the disease progresses. Although 16S rRNA metagenomics offers a comprehensive view of airway anaerobes, it is not routinely performed in clinical microbiology laboratories. This study aimed to evaluate the ability of routine sputum culture to identify strict anaerobes in people with CF (pwCF) compared to 16S rRNA sequencing, and to assess the impact of sample transport conditions. Sputum from 48 pwCF was analyzed by anaerobic culture and 16S rRNA sequencing. Strict anaerobes were detected in 95.8% of patients by culture and 100% by 16S rRNA sequencing. Culture identified 23 strict anaerobic species (mean 2.6 per sample), while 16S rRNA sequencing revealed nearly 100 species (mean 43 per sample). Importantly, culture isolated key genera such as Veillonella and Prevotella, core members of the CF airway anaerobiome. Transport conditions (aerobic vs. anaerobic) did not affect anaerobe detection. These new findings support changes in the processing of CF sputum in the everyday practice of clinical microbiology laboratories and promote the characterization of the culturable anaerobic airway microbiota.},
}

@article {pmid41720808,
year = {2026},
author = {Jin, Y and An, HJ and Zheng, TT and Li, JJ and Gao, JM and Zhong, XL and Li, BH and Liu, YY and Zhuang, XJ and Chen, JH and Rao, JH},
title = {Adenosine from high-fat-diet-tolerant monkey-derived Limsolactobacillus reuteri MacFasB02 modulates cholesterol metabolism to alleviate hyperlipidemia and inflammation.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00765-z},
pmid = {41720808},
issn = {2396-8370},
support = {82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 82471097 and 82200966//National Natural Science Foundation of China/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 2024GDASZH-2024010101//GDAS' Project of Science and Technology Development/ ; },
abstract = {Hyperlipidemia is a leading global health challenge, limited by the safety liabilities of current pharmacotherapies. Here, we isolated a novel Limosilactobacillus reuteri strain, MacFasB02, from fecal samples of cynomolgus monkeys tolerant to chronic high-fat diet (HFD). This study aimed to systematically evaluate its probiotic properties and therapeutic potential against hyperlipidemia. In vitro, MacFasB02 exhibited robust growth, acid production, and tolerance to acidic and bile environments. In HFD-fed mice, 13-week MacFasB02 administration reduced weight gain, serum triglycerides, low-density lipoprotein cholesterol and total cholesterol, while ameliorating hepatic steatosis and inflammation, as well as restoring intestinal barrier integrity by enhanced villus architecture, goblet cell function, and tight junction proteins expression. Metagenomic analysis revealed gut microbiota remodeling. Transcriptomic profiling coupled with in vivo validation demonstrated upregulation of Apoa1 and Pltp in cholesterol metabolism. Untargeted metabolomics integrated with whole-genome sequencing and supernatant metabolite profiling identified adenosine as a key MacFasB02-derived metabolite in purine metabolism. Consistently, In vitro experiments showed that adenosine reduced lipid accumulation and inflammation in hepatocytes by regulating Apoa1 and Pltp to modulate cholesterol metabolism. Collectively, MacFasB02 exerts dual lipid-lowering and anti-inflammatory effects probably via adenosine-mediated modulation of cholesterol metabolism, promising potential as a live biopharmaceutical agent for hyperlipidemia.},
}

@article {pmid41720311,
year = {2026},
author = {Liu, C and Ji, M and Wu, W and Shi, Y and Treu, L and Wang, W and Campanaro, S},
title = {Self-sufficient fermentation paradigm for cassava stillage valorization into C6 carboxylic acids: regulatory mechanisms and novel microbe identification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134236},
doi = {10.1016/j.biortech.2026.134236},
pmid = {41720311},
issn = {1873-2976},
abstract = {Cassava stillage (CS), a carbohydrate-rich byproduct of bioethanol production, holds significant untapped potential as a renewable resource. Upcycling this problematic wastewater offers great promise for addressing both environmental challenges and the demand for sustainable biochemicals. Here, this study proposed a self-sufficient biotechnological paradigm that directly valorizes CS into medium-chain carboxylic acids (MCCAs, e.g., caproic acid) by integrating lactic acid/butyric acid-type fermentation with microbial chain elongation (CE) by two phase fermentation regulatory. Lactic acid and butyric acid were regulated as dominant products with optimal ratio around 2 from CS degradation, and then chain elongated into caproic acid with optimal pH of 6. pH was found to play a crucial role in controlling product distribution in both phases of fermentation and shaping the microbiome. Meanwhile, chain elongation resilience was also found operational pH-dependent. Metagenomic analysis identified the bacterium Clostridium sp. BUCT163 as a putative lactic acid-driven chain elongating microbe. Whole-genome comparison between Clostridium sp. BUCT163 and Clostridium kluyveri species indicated that the genes encoding lactic acid conversion are not widespread among C. kluyveri populations. The combination of metagenomic-binning and comparative genomic analysis Clostridium sp. BUCT163 was distinguished as the novel potential lactic acid/ethanol-driven chain elongating microbe which successfully provided valuable data sets to link bacterial identities with chain elongating microbes. These findings provide foundation for the resource recovery process from CS in a self-sufficient anaerobic fermentation paradigm and the microbial management of chain elongating systems.},
}

@article {pmid41720310,
year = {2026},
author = {Zhao, W and Chen, P},
title = {Resilient biological nitrogen removal from surfactant-rich wastewater: construction of an indigenous community, quantitative tolerance assessment, and multi-level fault tolerance mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134251},
doi = {10.1016/j.biortech.2026.134251},
pmid = {41720310},
issn = {1873-2976},
abstract = {Linear alkylbenzene sulfonates (LAS) severely inhibit biological nitrogen removal. In this study, an indigenous microbial community (ICM) with heterotrophic nitrification-aerobic denitrification (HN-AD) capability was developed through long-term directed acclimatization. The ICM exhibited markedly enhanced resistance to LAS over a concentration range of 0-300 mg/L, maintaining nitrogen transformation rates more than twofold higher than those of conventional activated sludge. By integrating Haldane kinetic modeling with species sensitivity distribution analysis, we demonstrated that the ICM increased the 5% hazardous concentration (HC5) by 78%, thereby substantially expanding its ecological tolerance. Metagenomics and qPCR linked ICM resilience to multi-level responses; quorum sensing regulation, EPS-mediated sequestration, and enhanced redox homeostasis reinforced HN-AD performance. Dominant genera Pseudomonas and Aeromonas coupled detoxification with nitrogen removal. These findings demonstrate the ICM's transition from passive survival to active nitrogen removal reinforcement, offering quantitative benchmarks for resilient surfactant-rich wastewater treatment.},
}

@article {pmid41720032,
year = {2026},
author = {Kong, X and He, Y and Guo, J and Chen, Y and An, D},
title = {Chain-length-associated response patterns of chlorinated paraffins on activated sludge systems driven by microbial community response.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141542},
doi = {10.1016/j.jhazmat.2026.141542},
pmid = {41720032},
issn = {1873-3336},
abstract = {Chlorinated paraffins (CPs) are emerging contaminants detected in wastewater treatment plants, yet their impacts on activated sludge systems remain poorly understood. In this study, parallel sequencing batch reactors were employed to comprehensively evaluate the effects of short-chain (SCCP), medium-chain (MCCP), and long-chain (LCCP) CPs on pollutant removal performance, sludge properties, and microbial ecological responses. Under the tested nominal loading, the C24-LCCP standard led to a clear reduction in nitrogen removal efficiency, whereas MCCP and SCCP maintained stable or even enhanced phosphorus removal performance. CP exposure generally increased oxidative stress and cytotoxicity, while SCCP and MCCP further stimulated extracellular polymeric substances secretion, consistent with an enhanced floc/cell-interface protective phenotype. Metagenomic analysis revealed that SCCP and MCCP enriched genera (Acinetobacter, Dechloromonas, Zoogloea) associated with phosphorus removal and increased the abundance of key nitrogen transformation genes, whereas the C24-LCCP standard exhibited comparatively weaker shifts in functional gene profiles. Metatranscriptomic profiling indicated treatment-associated differences in transcriptional responses under the tested nominal loading, with SCCP showing the largest DEG set (>30,000 genes) in this dataset. Integrated metagenomic and metatranscriptomic analyses revealed a coordinated stress‑response program under SCCP, characterized by activation of efflux pumps, DNA repair, redox regulation, environmental stress responses, and biofilm-associated functions, together with elevated energy metabolism and ABC transporter signals. These molecular and community-level patterns aligned with the observed variations in treatment performance and sludge properties, providing convergent evidence for a chain-length-associated response framework. These findings provide comparative molecular and phenotypic evidence that may inform future risk assessment and hypothesis-driven mitigation studies on CP impacts in biological wastewater treatment systems.},
}

@article {pmid41719987,
year = {2026},
author = {Dang, X and Xu, S},
title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119906},
doi = {10.1016/j.ecoenv.2026.119906},
pmid = {41719987},
issn = {1090-2414},
abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.},
}

@article {pmid41719533,
year = {2026},
author = {Ippolito, I and Hug, L},
title = {Antimicrobial resistance gene diversity, prevalence, and mobility within four landfills.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0226},
pmid = {41719533},
issn = {1480-3275},
abstract = {Antibiotics in landfills create selection pressures on the microorganisms present, selecting for antibiotic resistance genes (ARGs) and antibiotic resistant organisms (ARO). The aim of this study was to assess whether landfills are hot-spots of antimicrobial resistance and whether landfills may contribute to global ARO diversity through ARG lateral gene transfer. Genome resolved metagenomic sequencing combined with sequence-search-based and deep learning tools were used to determine ARG diversity and prevalence from four active municipal landfills and their adjacent ground or surface water systems. Comparison to pristine and anthropogenic environments highlighted that landfill microbial communities contain distinct ARG signatures, including a broader diversity of ARGs. Plasmids made up 4.1-8.4% of assembled scaffolds and carried 5.4-12.0% of the identified ARGs in assembled data, depending on the sample type. Enriched ARG resistance mechanisms on mobile elements included multidrug resistance and antibiotic inactivation. The results indicate that landfills house a high diversity of antimicrobial resistance mechanisms and drug classes, with a moderate fraction encoded on mobile elements. Landfills are thus likely mixing grounds for ARG transfer and evolution of novel or augmented ARO lineages.},
}

@article {pmid41719397,
year = {2026},
author = {Cheng, G and Jiang, X and Zhu, L and Chen, X and Liu, R and Zhu, L and Hu, X and Zhang, S and Tan, W and Lin, D and Zhang, L and Wu, C and Li, M},
title = {Intratumoral Parvimonas micra promotes esophageal squamous cell carcinoma via p-cresol-induced Treg differentiation.},
journal = {Science advances},
volume = {12},
number = {8},
pages = {eady1644},
pmid = {41719397},
issn = {2375-2548},
mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/microbiology/pathology/immunology/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Esophageal Neoplasms/microbiology/pathology/immunology/metabolism ; Tumor Microenvironment/immunology ; *Cresols/metabolism ; *Cell Differentiation/drug effects ; Animals ; Mice ; Female ; *Bacillota ; Male ; Prognosis ; Cell Line, Tumor ; Reactive Oxygen Species/metabolism ; },
abstract = {Intratumoral microbiota has emerged as a notable factor influencing cancer initiation and progression. However, its composition and functional impact in esophageal squamous cell carcinoma (ESCC) remain largely unexplored. Here, we performed metagenomic sequencing on 119 paired tumor-normal tissues from patients with ESCC and single-cell RNA sequencing on 45 samples to investigate microbe-host interactions. We identified Parvimonas micra (P. micra), an anaerobic oral-derived bacterium, as significantly enriched in tumor tissues and associated with poor prognosis. Moreover, the abundance of P. micra correlated with increased regulatory T cell (Treg cell) infiltration in the ESCC tumor microenvironment. Through cellular and animal experiments, we demonstrate that P. micra promotes tumor growth by secreting p-cresol, a metabolite of amino acid fermentation, which elevates reactive oxygen species levels and induces FOXP3[+] Treg differentiation, thereby fostering immunosuppression and tumor growth. Our study establishes a mechanistic link between intratumoral microbiota and the immune microenvironment, highlighting the microbial contribution to ESCC progression and prognosis.},
}

Humans
*Esophageal Squamous Cell Carcinoma/microbiology/pathology/immunology/metabolism
*T-Lymphocytes, Regulatory/immunology/metabolism
*Esophageal Neoplasms/microbiology/pathology/immunology/metabolism
Tumor Microenvironment/immunology
*Cresols/metabolism
*Cell Differentiation/drug effects
Animals
Mice
Female
*Bacillota
Male
Prognosis
Cell Line, Tumor
Reactive Oxygen Species/metabolism

@article {pmid41719263,
year = {2026},
author = {Huang, G and Gallagher, TL and Tsongalis, GJ and Lefferts, JA},
title = {Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0341560},
pmid = {41719263},
issn = {1932-6203},
mesh = {Humans ; *DNA, Fungal/genetics/analysis ; *DNA, Bacterial/genetics/analysis ; *Multiplex Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; *Fungi/genetics ; DNA, Ribosomal/genetics ; Bacteria/genetics ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Molecular methods in clinical and research applications frequently encounter complex mixtures of human and microbial DNA, sometimes alongside environmental or reagent contaminants. In metagenomic studies, the presence of host contamination poses a significant challenge, reducing the assay sensitivity of microbial detection and characterization. Different host-depletion and microbial enrichment platforms have been developed to reduce or eliminate host DNA in samples predominantly composed of human DNA. To establish an effective method to assess the efficacy of host DNA depletion or microbial enrichment platforms, this study aimed to develop a multiplex, broad-range 16S/18S ribosomal DNA droplet digital PCR (rDNA ddPCR) assay capable of simultaneously quantifying bacterial and fungal DNA, along with a human housekeeping gene, RPP30 (Ribonuclease P/MRP Subunit P30). Genomic DNA from key representatives of Gram-positive bacteria, Gram-negative bacteria, and fungi was tested in broad-range 16S/18S rDNA duplex (16S/RPP30 or 18S/RPP30) and triplex (16S/18S/RPP30) ddPCR assays to determine optimal assay conditions, specificity, and sensitivity. This assay demonstrated high sensitivity, specificity, and reproducibility, with detection limits of approximately 3 copies/µL for the 16S target (0.5 pg Staphylococcus aureus gDNA) and 1-2 copies/µL for the 18S target (16 fg of Candida albicans gDNA) in both duplex and triplex formats. Within a defined range, a linear relationship was observed between microbial DNA input and 16S/18S rDNA copy number by ddPCR. Furthermore, different commercial ddPCR master mixes had contrasting effects on the amplitudes of positive 16S/18S droplet clusters. As a proof of concept for the assay's utility in metagenomic studies, we demonstrated that one extraction kit achieved more efficient depletion of human DNA and better enrichment of microbial DNA. In summary, we developed a multiplex, broad-range 16S/18S ddPCR assay with high sensitivity and specificity, which holds promise as a QA/QC (Quality Assurance/Quality Control) platform in metagenomic studies and other research settings.},
}

Humans
*DNA, Fungal/genetics/analysis
*DNA, Bacterial/genetics/analysis
*Multiplex Polymerase Chain Reaction/methods
RNA, Ribosomal, 16S/genetics
Sensitivity and Specificity
*Fungi/genetics
DNA, Ribosomal/genetics
Bacteria/genetics
RNA, Ribosomal, 18S/genetics

@article {pmid41719150,
year = {2026},
author = {Ni, Y and Wang, Y},
title = {ICTV Virus Taxonomy Profile: Nipumfusiviridae 2026.},
journal = {The Journal of general virology},
volume = {107},
number = {2},
pages = {},
doi = {10.1099/jgv.0.002226},
pmid = {41719150},
issn = {1465-2099},
mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Phylogeny ; Virion/ultrastructure/genetics ; *Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure ; Capsid Proteins/genetics/chemistry ; },
abstract = {The family Nipumfusiviridae includes DNA viruses with hosts deduced to be marine ammonia-oxidizing archaea, specifically those in the archaeal family Nitrosopumilaceae. Virus genomes have been discovered through metagenomics of samples from inlets, coastal areas, intertidal zones, epipelagic and oceanic waters, and soil. Viruses have neither been isolated nor enriched through experiments. The family Nipumfusiviridae includes several genera. The virions of nipumfusiviruses are predicted to have spindle-shaped morphology based on the analysis of the deduced structural models of the major capsid protein. Limited information can be provided about translation and replication from the genome. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Nipumfusiviridae, which is available at ictv.global/report/nipumfusiviridae.},
}

Genome, Viral
*DNA Viruses/classification/genetics/ultrastructure/isolation & purification
Phylogeny
Virion/ultrastructure/genetics
*Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure
Capsid Proteins/genetics/chemistry

@article {pmid41719127,
year = {2026},
author = {Wang, S and Su, LY and Lan, D and Pan, H and Xiong, M and Yao, M and Deng, Y and Fan, Z and Cao, Y and Zhou, H},
title = {Adenosine signaling driven by the gut microbiota underlies chronic alcohol-induced anesthetic resistance.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117015},
doi = {10.1016/j.celrep.2026.117015},
pmid = {41719127},
issn = {2211-1247},
abstract = {Chronic alcohol consumption increases anesthetic tolerance, yet the underlying in vivo mechanisms remain unclear. Here, we demonstrate that long-term alcohol exposure reduces anesthetic efficacy in both humans and mice, prolonging induction and shortening maintenance. Fecal microbiota transplantation from alcohol-exposed donors recapitulated this phenotype in naive mice, indicating a causal role of gut microbiome alterations. Metagenomic and metabolomic analyses identified elevated adenosine as a key microbiota-derived metabolite. Adenosine supplementation decreased anesthetic sensitivity, likely via downregulation of gamma-aminobutyric acid (GABA) receptors. Our findings reveal a gut microbiota-adenosine pathway mediating alcohol-induced anesthetic resistance.},
}

@article {pmid41718326,
year = {2026},
author = {Hernández-Cruz, E and Gómez-Godínez, LJ and Ruvalcaba-Gómez, JM and Arteaga-Garibay, RI},
title = {Optimized Method for Efficient DNA Extraction from Agricultural Soils.},
journal = {Methods and protocols},
volume = {9},
number = {1},
pages = {},
pmid = {41718326},
issn = {2409-9279},
abstract = {Soil harbors the highest concentration of microorganisms in ecosystems, and their molecular characterization through high-throughput sequencing is essential for metagenomic studies. However, obtaining high-quality, high-concentration DNA is limited by physicochemical properties (pH, heavy metals, humic acids) and adsorption to clay minerals. Although standardized commercial protocols exist, they present variable limitations depending on soil type. This study developed and validated the National Center for Genetic Resources-Microorganism Collection (CNRG-CM) method, which incorporates innovative pre-washing steps using phosphate-buffered saline (PBS) and sodium phosphate to effectively remove inhibitory humic acids and metal ions, combined with cetyltrimethylammonium bromide (CTAB)/chloroform extraction to achieve high-molecular-weight metagenomic DNA isolation. The CNRG-CM method was applied to three diverse soil types with variable physicochemical properties, recovering DNA concentrations ranging from 1000 to 1300 ng/μL ith a yield of 30 to 48 µg/g[-1], significantly exceeding those obtained with a standard commercial kit with maximum DNA concentrations of 360 ng/μL and a yield of 43 µg/g[-1]. The CNRG-CM protocol is established as an effective and adaptable alternative for metagenomic DNA extraction across diverse agricultural and ecological contexts. It enables subsequent metagenomic studies of soil microbial communities.},
}

@article {pmid41718052,
year = {2026},
author = {La Via, L and Ferlito, S and Di Modica, MS and Marino, A and Nunnari, G and Cacopardo, B and Lechien, JR and Lentini, M and Lavalle, S and Botto, GC and Buscema, P and Gruppuso, L and Maniaci, A},
title = {The Global Impact of Sepsis: Epidemiology, Recognition, Management, and Health System Challenges.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {7},
number = {1},
pages = {},
pmid = {41718052},
issn = {2673-3986},
abstract = {BACKGROUND: Sepsis constitutes a major healthcare burden worldwide, with an estimated 48.9 million incident cases and 11.0 million deaths in 2017, accounting for nearly one-fifth of all global deaths. Even with advances in definitions and guidelines, significant inequalities persist in awareness, early treatment, and health system readiness.

METHODS: We performed a structured narrative review of epidemiology studies, clinical case definitions, diagnostic approaches, stewardship interventions, and health system reports. Both electronic sources (PubMed, Web of Science, Embase, Scopus) and grey literature (World Health Organization [WHO], National Institute for Health and Care Excellence [NICE], Society Critical Care [SSC]) were explored. Evidence incorporated themes were organized across recognition, diagnostics, antimicrobial therapy, organ support, guidelines, and health system determinants.

RESULTS: Measurement tools, including quick Sequential Organ Failure Assessment (qSOFA) and Sequential Organ Failure Assessment (SOFA), exhibited suboptimal sensitivity and utility in varied clinical environments. Biomarkers (procalcitonin, presepsin, CD64) and rapid molecular diagnostics, including metagenomic next-generation sequencing (mNGS) and AI-based devices, enhance detection but are limited by cost and infrastructure constraints. Each hour of delay in antibiotic therapy is associated with a 6-10% increased risk of mortality, underscoring the importance of stewardship, including the incorporation of empiric regimens with rapid de-escalation. Health system bottlenecks-human resources, funding, infrastructure-continue to be a significant determinant of outcomes, especially in low- and middle-income countries.

CONCLUSIONS: Attaining the 2030 WHO targets for sepsis involves precision diagnostics, adaptable guidelines, stewardship frameworks, and resilient health systems. Fair application and resource allocation are crucial to lower the incidence and mortality worldwide.},
}

@article {pmid41717629,
year = {2026},
author = {Wang, X and Yang, Y and Li, Y and Zhu, Z and Khashaba, R and Yue, Q},
title = {Multi-omics reveals microbial community characteristics and flavonoid biotransformation mechanisms during mung bean sour fermentation.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101342},
pmid = {41717629},
issn = {2665-9271},
abstract = {Fermented foods are gaining popularity for their health benefits, and fermented mung bean products are recognized for their nutritional value. To investigate microbial community succession and abundance dynamics of bioactive compounds like flavonoids in fermented mung bean sour (MBS), parallel metagenomic and metabolomic analyses were performed. Metagenomic profiling identified Lactiplantibacillus, Lactococcus, Bifidobacterium, and Acetobacter as dominant genera. Functional gene analysis demonstrated a significant increase in the relative abundance of flavonoid degradation pathways, which exhibited strong positive correlations (r > 0.8, p < 0.05) with the dominant genera. Metabolomic analysis revealed a significant decrease in flavonoids, including vitexin and orientin. Moreover, increased activities of β-glucosidase and α-rhamnosidase were identified as key factors promoting the biotransformation of flavonoids into bioactive metabolites such as apigenin, naringenin, and quercetin. This study provides a foundation for further understanding the microbial conversion and utilization of flavonoid compounds in mung beans.},
}

@article {pmid41717089,
year = {2025},
author = {Shi, S and Qi, J and Peng, W and Su, X and Chen, P and Xu, S and Li, S and Ma, L and Wang, W and Jiang, K and Liu, Z and Li, W and Xiong, H and Wang, Y},
title = {Convergent gut microbiome adaptation and pervasive antibiotic resistome in Qinghai-Tibet Plateau passerines.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733974},
pmid = {41717089},
issn = {1664-302X},
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau, an extreme high-altitude ecosystem, presents a unique model for studying host-microbe-environment coevolution under environmental stress. However, the role of resident wildlife, particularly non-migratory passerines, as reservoirs and vectors for cross-boundary antibiotic resistance gene (ARG) dissemination remains poorly understood.

METHODS: Here, through metagenomic analysis of two endemic passerines (Pseudopodoces humilis and Pyrgilauda ruficollis) and their habitats.

RESULTS: We reveal convergent adaptations in their gut microbiomes, dominated by Actinomycetota, Pseudomonadota and Bacillota. Functional enrichment in carbohydrate metabolism and genetic information processing underpins host energy optimization in extreme high-altitude environments. Critically, these birds constitute a major reservoir of ARGs, harboring 153 antibiotic resistance ontologies (AROs) with nearly universal resistance to clinical antibiotic classes. The core resistome-comprising glycopeptide (van clusters), fluoroquinolone, and tetracycline resistance genes-reflects anthropogenic contamination amplified by environmental persistence. Environmental transmission pathways were unequivocally demonstrated via 47 AROs shared between avian hosts and proximal matrices (soil/grass), coupled with livestock-derived antibiotic influx through excreta, establishing the plateau as a hotspot for resistance gene flux. Strikingly, "low-abundance-high-resistance" taxa (Pseudomonadota, Actinomycetota, and Bacillota; ≤30% abundance but >80% ARG contribution) drive resistome plasticity, potentially facilitated by horizontal gene transfer.

DISCUSSION: Our findings redefine resident passerines as sentinels of ecosystem health and bridges for cross-boundary antimicrobial resistance (AMR) spread. Mitigating global AMR thus necessitates interdisciplinary strategies targeting environmental reservoirs (e.g., regulating livestock antibiotic use) and monitoring avian-mediated gene flow.},
}

@article {pmid41716893,
year = {2026},
author = {Cao, Y and Huang, J and Wu, W and Xu, Z and Wang, C and Wu, X and Zhan, C and Xing, J and Liu, J and Zhu, M and Ma, S},
title = {Clinical Utility and Therapeutic Strategy Value of Metagenomic Next-Generation Sequencing in Pulmonary Infection Among Cancer Patients.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {568562},
pmid = {41716893},
issn = {1178-6973},
abstract = {INTRODUCTION: Cancer patients, particularly those with lung cancer, are highly susceptible to pulmonary infections due to both the disease itself and the immunosuppressive effects of treatments such as chemotherapy and immunotherapy. The objective of this study was to analyze pathogenic distribution characteristics of pulmonary infections in cancer patients and evaluated the guidance of metagenomic next-generation sequencing (mNGS) on clinical administration.

METHODS: This retrospective study included 66 samples from cancer patients. Pathogens in patient specimens, encompassing peripheral blood, bronchoalveolar lavage fluid (BALF), sputum, and other samples, were identified using both mNGS and culture methods.

RESULTS: Compared to culture methods, mNGS demonstrated a sensitivity of 95.5% across all samples. In terms of overall detections, Human gammaherpesvirus 4 was identified as the most frequently detected pathogen in cancer patients, while Escherichia coli and Candida albicans were ranked as the most common bacterial and fungal pathogens, respectively. During the perioperative period, non-surgical short-term treatment, non-surgical long-term treatment, and long-term treatment groups, Escherichia coli and Achromobacter xylosoxidans were all identified. Moreover, the treatment strategies for patients were timely adjusted based on the mNGS results, resulting in a significant improvement in clinical symptoms for 59.3% (16 out of 27) of the cancer patients.

CONCLUSION: mNGS is an advanced approach for pathogen detection in cancer patients, with commendable diagnostic performance demonstrated. The results of mNGS contribute to the rapid modification of clinical medication, which may improve the survival rate of cancer patients.},
}

@article {pmid41716871,
year = {2026},
author = {Rosenqvist, T and Cleary, M},
title = {Detecting "invisible" Phytophthora lineages in publicly available sequencing data.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag019},
pmid = {41716871},
issn = {2730-6151},
abstract = {Our understanding of microbial eukaryotic diversity is limited by biases induced by cultivation and DNA-amplification. Microbial lineages which are challenging or impossible to culture and develop universal metabarcoding primers for can be considered "invisible." These "invisible" microbes can however be detected in genomic and metagenomic sequencing datasets. This study introduces a new pipeline for targeted assembly of internal transcribed spacer (ITS) sequences from genomes and metagenomes (https://github.com/tage-ro/denim), which provides advantages in sensitivity and precision over comparable marker-gene assembly software. It further shows how publicly sequencing datasets can be screened for the genus Phytophthora, which includes economically and ecologically devastating plant pathogens. Analysis of 104 sequencing datasets resulted in 733 full ITS sequences, 1626 ITS1 sequences and 2191 ITS2 sequences associated with a variety of eukaryotic lineages. Phytophthora ITS sequences associated with known species in clades 1, 2, 4, 6, 7 and 8 were assembled, along with sequences only distantly related to known taxa. In addition, it provided potential indications of new pathogen-host interactions, with potential impacts on agriculture and human health. This study presents a new approach towards discovering and detecting "invisible" microbes, thus expanding our understanding of microbial eukaryotic diversity. Moreover, it allows detection and monitoring of new host-microbe interactions, and characterizing the geographic distribution of cultured and uncultured microorganisms.},
}

@article {pmid41716833,
year = {2026},
author = {Xie, F and Li, J and Liu, P and Xu, L and Wang, Y and Qiu, Q and Mao, S},
title = {Genome-resolved metagenomics reveals gastrointestinal microbiome adaptations in sheep responding to fiber- and starch-rich diets.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {24},
number = {},
pages = {233-245},
pmid = {41716833},
issn = {2405-6383},
abstract = {The gastrointestinal tract of ruminants hosts a specialized microbial ecosystem that has evolved to efficiently digest fiber. However, modern intensive farming practices, which often involve reduced dietary fiber and increased grain supplementation, are linked to metabolic disorders in ruminants. Despite this, the understanding of the taxonomic and functional adaptations of the gastrointestinal microbiome to dietary changes remains limited, largely due to the challenges in obtaining high-resolution characterization of microbial communities. This study employed genome-resolved metagenomics to examine how a starch-rich (SR) grain-based diet compares to a fiber-rich (FR) hay-based diet in shaping the composition and function of the gastrointestinal microbiome in the rumen, jejunum, and cecum of Hu sheep. A total of 10 sheep (approximately 180 d old, with a body weight of 25.6 ± 0.41 kg) were allocated to the 2 dietary groups (SR and FR groups) for a 28-d experimental period, and metagenomic sequencing was performed on digesta samples from different gastrointestinal regions. Using a representative microbial gene catalog (RGMGC) and 10,373 metagenome-assembled genomes from previous studies,microbial composition, strain-level diversity, and carbohydrate-active enzyme profiles at higher taxonomic and functional resolution were analyzed. The results showed that the transition from the FR diet to the SR diet significantly altered the fermentation patterns and the structure and function of the sheep gastrointestinal microbiota. Community analysis revealed microbial taxa such as Prevotella spp., Alistipes spp., RC9 spp., CAG-110 spp., and Akkermansia spp. with significantly altered abundances (P < 0.05), primarily associated with the reduced fiber content in the SR diet. Moreover, the gastrointestinal microbiome exhibited strain-level changes in carbohydrate degradation, leading to reduced metabolic functions necessary for fiber processing. Comparative genomics at the single-genome level pinpointed Prevotella as a core genus with strains showing significant functional differences, notably in the capacity to degrade plant polysaccharides. Overall, these findings provide new insights into microbial regulation of gastrointestinal health and offer valuable enzyme gene resources in ruminants.},
}

@article {pmid41716274,
year = {2026},
author = {Name, PE and Tibiri, EB and Tiendrébéogo, F and Sawadogo, S and Djigma, F and Traoré, L and Eni, AO and Pita, JS},
title = {Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1722370},
pmid = {41716274},
issn = {1664-302X},
abstract = {Sweetpotato is a key crop for global food security, particularly in Burkina Faso, where its productivity is increasingly threatened by viral diseases, especially those caused by CRESS-DNA viruses. However, the diversity of these viruses in Burkina Faso remains poorly characterized due to limitations of conventional diagnostic approaches. In this study, nanopore sequencing was used to investigate the diversity of CRESS-DNA viruses infecting sweetpotato in Burkina Faso. Ninety-eight symptomatic dried leaf samples from a previously established biobank were selected and analyzed. Total DNA was extracted, enriched using rolling circle amplification (RCA), and sequenced using the MinION Mk1C platform. In parallel, RNA viruses were also investigated using nanopore sequencing. RCA successfully amplified 53 of the 98 samples, from which 28 complete and 25 partial CRESS-DNA virus genomes were recovered. Sequence analyses revealed high genomic diversity, with sweet potato leaf curl virus (SPLCV) being the most prevalent. Sweet potato symptomless virus 1 (SPSMV-1) was detected for the first time in Burkina Faso in a co-infection with SPLCV. Additionally, 52 deltasatellite genomes (50 complete, 2 partial) were identified in association with SPLCV, displaying approximately 86% nucleotide identity with known sequences, suggesting the presence of genetically distinct putative deltasatellites. RNA virome analysis revealed frequent co-infections involving sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus, with SPFMV commonly co-occurring with SPLCV. Four complete SPFMV genomes were recovered and clustered within phylogroup B, forming a distinct subclade. Overall, this study highlights the remarkable diversity of viruses infecting sweetpotato in Burkina Faso and reports, for the first time, the presence of SPSMV-1 and sweepovirus-associated deltasatellites in the country. These findings underscore the importance of ongoing molecular surveillance to support effective viral disease management strategies and food security.},
}

@article {pmid41716262,
year = {2026},
author = {Qiao, YC and Jiang, XX and Zan, JP and Chen, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG},
title = {Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1691984},
pmid = {41716262},
issn = {1664-302X},
abstract = {BACKGROUND AND AIMS: Mulching is a widely used agricultural management practice with profound effects on soil properties and crop productivity. However, its impact on soil microbial community structure and function remains insufficiently understood. This study aimed to investigate how different mulching treatments influence the composition, functional potential, and interaction networks of soil microbial communities in a chieh-qua-legume rotation system.

METHODS: Metagenomic sequencing was employed to analyze soil samples subjected to four mulching treatments (biodegradable mulch, non-degradable silver mulch, non-degradable black mulch, and straw mulch) as well as a no-mulch control (CK).

RESULTS: Mulching treatments significantly altered soil microbial diversity and community structure, with straw and biodegradable mulches supporting higher diversity than the control. Biodegradable mulch was strongly correlated with changes in soil pH and enriched denitrifying bacteria such as Thauera and Comamonadaceae, while reducing the abundance of genes related to energy metabolism and carbon fixation. These findings suggest that organic carbon from mulch degradation may enhance denitrification, potentially leading to nitrogen loss. Co-occurrence network analysis revealed that biodegradable mulch promoted more complex and connected microbial networks, whereas plastic mulches resulted in simpler structures. Additionally, all mulching treatments significantly reduced the abundance of the autotrophic ammonia-oxidizing archaeon Thaumarchaeota, likely due to reduced soil oxygen under mulch.

CONCLUSION: This study provides new insights into how different mulching practices modulate soil microbial communities and their ecological functions. The results underscore the importance of tailoring mulching strategies to maintain soil health and fertility. Specifically, nitrogen supplementation is recommended when using biodegradable mulch in chieh-qua cultivation systems.},
}

@article {pmid41628857,
year = {2026},
author = {Theodosiou, AA and Bogaert, D and Cleary, DW and Fady, PE and Feehily, C and Gilbert, JA and Greenhough, B and Guardabassi, L and Hall, LJ and Harman, T and Kuijper, EJ and Lebeer, S and Lorimer, J and Spector, TD and Jones, CE},
title = {Microbiome research in practice: priorities for clinical translation and impact.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.01.021},
pmid = {41628857},
issn = {1469-0691},
abstract = {BACKGROUND: Rapid advances in microbiome science have sparked clinical and commercial enthusiasm for interventions, yet translation into practice risks outpacing both mechanistic understanding and the infrastructure required for safe adoption.

OBJECTIVES: To outline a coordinated research, clinical, social, and policy agenda for advancing safe, effective, and equitable microbiome-based interventions.

SOURCES: We convened an interdisciplinary Royal Society-funded expert workshop (Leeds, UK, October 2024) with international leaders in microbiome science, clinical trials, regulation, and social science. Thematic analysis of workshop discussions and written contributions identified priority domains for translation.

CONTENT: Three intersecting priorities emerged: scientific credibility, practical viability, and stakeholder engagement. Scientific credibility demands investment in multiomic and strain-level characterization of host-microbiome interactions on a large scale, benchmarking of clinical and microbiological endpoints, and harmonization of trial conduct and reporting. Clinical adoption requires fit-for-purpose regulation, diversified investment to address funding bottlenecks, and coordinated capacity building. Meaningful stakeholder engagement with clinicians, patients, policymakers, and the public is essential to foster confidence, develop clinically relevant research questions, and ensure equitable implementation of any new technology.

IMPLICATIONS: To realize the clinical impact of microbiome interventions, sustained collaboration across disciplines is essential. This review offers a translational roadmap and actionable priorities to accelerate safe, effective, and equitable microbiome-based interventions-ensuring the field fulfils its clinical potential and delivers real-world impact.},
}

@article {pmid41716172,
year = {2025},
author = {Nazerke, K and Ruslan, A and Saule, D and Aida, D and Svetlana, V},
title = {Advances and emerging technologies in the diagnosis of viral infections in pigs: Progress, challenges, and One Health perspectives.},
journal = {Veterinary world},
volume = {18},
number = {12},
pages = {3788-3805},
pmid = {41716172},
issn = {0972-8988},
abstract = {Viral infections continue to pose major challenges to pig health, farm productivity, and global food security. Early and accurate diagnosis is the cornerstone of disease prevention, surveillance, and control in swine populations. In recent years, remarkable progress has been achieved in molecular, serological, and digital diagnostic technologies, enabling more rapid, sensitive, and field-adaptable detection of important porcine viruses such as African swine fever virus, porcine reproductive and respiratory syndrome virus, and classical swine fever virus. This review summarizes current and emerging diagnostic approaches, highlighting polymerase chain reaction (PCR) and its advanced forms, quantitative PCR and digital PCR, as the gold standards for laboratory confirmation. The advent of next-generation sequencing and metagenomics has revolutionized pathogen discovery and genomic surveillance, providing comprehensive insights into viral evolution and transboundary transmission. Isothermal amplification techniques such as loop-mediated isothermal amplification and recombinase polymerase amplification have shown strong potential for on-farm diagnosis due to their simplicity, rapidity, and minimal equipment requirements. Innovations such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated-based assays, biosensors, lab-on-a-chip platforms, and point-of-care testing devices are bridging the gap between laboratory precision and field application, allowing rapid decision-making during outbreaks. The integration of artificial intelligence, machine learning, and geographic information systems has further enhanced diagnostic interpretation, real-time data sharing, and early outbreak prediction under the One Health framework. Despite these advances, challenges remain in ensuring assay standardization, affordability, and equitable access in resource-limited regions. Continued international collaboration, data sharing, and policy harmonization under the guidance of the Food and Agriculture Organization, the World Organization for Animal Health, and the World Health Organization are essential for the global control of swine viral diseases. Ultimately, combining molecular innovation with digital adaptability offers the most promising path toward resilient, cost-effective, and sustainable diagnostic systems for safeguarding animal and public health.},
}

@article {pmid41715924,
year = {2026},
author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K},
title = {Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2026.02.022},
pmid = {41715924},
issn = {1542-0086},
abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared to archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.},
}

@article {pmid41715245,
year = {2026},
author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD},
title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {22},
pmid = {41715245},
issn = {2524-4671},
abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.

RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.

CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.},
}

@article {pmid41629500,
year = {2026},
author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y},
title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6991},
pmid = {41629500},
issn = {2045-2322},
support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; },
abstract = {UNLABELLED: Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38558-9.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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