@article {pmid41864063,
year = {2026},
author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J},
title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.},
journal = {EBioMedicine},
volume = {126},
number = {},
pages = {106224},
pmid = {41864063},
issn = {2352-3964},
mesh = {Humans ; *Parkinson Disease/microbiology/blood/diagnosis ; Disease Progression ; Male ; Female ; Aged ; Biomarkers/blood ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; Whole Genome Sequencing ; *Bacteria/genetics/classification ; Metagenomics/methods ; },
abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.

METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.

FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.

INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.

FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.},
}

Humans
*Parkinson Disease/microbiology/blood/diagnosis
Disease Progression
Male
Female
Aged
Biomarkers/blood
Middle Aged
Cross-Sectional Studies
*Microbiota
Whole Genome Sequencing
*Bacteria/genetics/classification
Metagenomics/methods

@article {pmid41957864,
year = {2026},
author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F},
title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00886-8},
pmid = {41957864},
issn = {2524-6372},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.

RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.

CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.},
}

@article {pmid41957950,
year = {2026},
author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A},
title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.},
journal = {Oncoimmunology},
volume = {15},
number = {1},
pages = {2656514},
doi = {10.1080/2162402X.2026.2656514},
pmid = {41957950},
issn = {2162-402X},
mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; },
abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.},
}

*Oncolytic Virotherapy/methods
Humans
Animals
Mice
*Adenoviridae/genetics
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
*Oncolytic Viruses
Feces/microbiology
Female
*Neoplasms/therapy/microbiology
Male

@article {pmid41958036,
year = {2026},
author = {Shin, H and Jeon, MK and Hur, HG},
title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70327},
doi = {10.1111/1758-2229.70327},
pmid = {41958036},
issn = {1758-2229},
support = {RS-2023-NR076613//National Research Foundation of Korea/ ; },
mesh = {*beta-Lactamases/genetics ; Metagenomics/methods ; *Bacteria/genetics/drug effects/enzymology/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Metagenome ; *Bacterial Proteins/genetics ; Microbiota ; Drug Resistance, Bacterial/genetics ; },
abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.},
}

*beta-Lactamases/genetics
Metagenomics/methods
*Bacteria/genetics/drug effects/enzymology/isolation & purification/classification
Anti-Bacterial Agents/pharmacology
Wastewater/microbiology
Metagenome
*Bacterial Proteins/genetics
Microbiota
Drug Resistance, Bacterial/genetics

@article {pmid41958322,
year = {2026},
author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B},
title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.},
journal = {American journal of primatology},
volume = {88},
number = {4},
pages = {e70148},
doi = {10.1002/ajp.70148},
pmid = {41958322},
issn = {1098-2345},
support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; },
abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.},
}

Animals
*Gastrointestinal Microbiome
*Macaca/virology/microbiology
*Virome
Tibet
Male
Animals, Zoo/virology
Female

@article {pmid41958469,
year = {2026},
author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A},
title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.},
journal = {Alzheimer's & dementia (New York, N. Y.)},
volume = {12},
number = {2},
pages = {e70239},
pmid = {41958469},
issn = {2352-8737},
abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.

METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.

RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).

DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.},
}

@article {pmid41958710,
year = {2026},
author = {Nakamichi, K and Manandhar, A and Shrestha, S and Sundararajan, M and Poudel, MP and Karmacharya, BM and Bade, A and Banjara, P and Shrestha, A and Sandt, A and Turski, G and Buhr, ED and Chowdhary, A and Van Gelder, RN},
title = {Association of Seasonal Hyperacute Panuveitis Syndrome with S. pneumoniae Endophthalmitis.},
journal = {Ophthalmology science},
volume = {6},
number = {5},
pages = {101128},
pmid = {41958710},
issn = {2666-9145},
abstract = {PURPOSE: To identify potential infectious agents in cases of seasonal hyperacute panuveitis syndrome (SHAPU) from vitreous biopsies of patients with this disorder.

DESIGN: A retrospective cohort analysis.

SUBJECTS: Vitreous biopsies were obtained during the course of care from 53 subjects with SHAPU.

METHODS: DNA extraction and whole genome shotgun sequencing was performed using Oxford Nanopore long read sequencing. Sequences were matched against microbial and human databases. Visual outcomes at presentation and at 6 months were recorded.

MAIN OUTCOME MEASURES: Identification and characterization of metagenomic sequences in vitreous isolates from subjects with SHAPU.

RESULTS: Adequate DNA for sequencing was obtained from 32 SHAPU subjects. Fifteen samples yielded bacteria on culture, with 14 S. pneumoniae and 1 S. aureus isolate recovered. Bacterial DNA was detected by whole genome sequencing in 29 of 32 cases. S. pneumoniae was the predominant organism recovered. Bacterial genomic loads ranged up to 10 000 bacteria/human cell, indicating active infection. No pathogens were detected in control samples. Reconstruction of bacterial genome was possible in 7 SHAPU cases and indicated diverse S. pneumoniae subtypes associated with individual cases. Sufficient DNA remained for analysis of torque teno virus by qualitative polymerase chain reaction in 17 cases, of which 13 were positive. Visual outcomes were mixed, with 7 patients having hypotonous eyes at 6 months, but 8 patients having better than 20/200 vision. No relationship could be discerned between presenting bacterial load and visual outcome.

CONCLUSIONS: The majority of SHAPU cases show molecular evidence for concurrent S. pneumoniae infection. Good visual results are possible in treating SHAPU as endophthalmitis.

FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.},
}

@article {pmid41959051,
year = {2026},
author = {Weng, Y and Moyne, O and Walker, C and Haddad, E and Lieng, C and Chin, L and Rahman, G and McDonald, D and Knight, R and Zengler, K},
title = {A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.710980},
pmid = {41959051},
issn = {2692-8205},
abstract = {Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.},
}

@article {pmid41959121,
year = {2026},
author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A},
title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.03.715941},
pmid = {41959121},
issn = {2692-8205},
abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.

OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.

METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.

MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.

CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.},
}

@article {pmid41959210,
year = {2026},
author = {Muller, E and Baum, S and Borenstein, E},
title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714614},
pmid = {41959210},
issn = {2692-8205},
abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.

RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.

AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL .},
}

@article {pmid41959308,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.711154},
pmid = {41959308},
issn = {2692-8205},
abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.

IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

@article {pmid41959338,
year = {2026},
author = {Kramer, AM and Zhang, A and Ayala, N and de Sanctis, B and Karim, L and Hinrichs, AS and Walia, S and Turakhia, Y and Corbett-Detig, R},
title = {Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.29.711974},
pmid = {41959338},
issn = {2692-8205},
abstract = {Pangenomes capture population-level variation but remain computationally challenging at scale. We present Panmap, a tool that leverages evolutionary structure to place, align, and genotype sequencing reads against mutation-annotated pangenomes containing up to millions of genomes. Panmap introduces a phylogenetically compressed k -mer index that stores only sequence differences along branches, enabling efficient comparison of reads to both sampled genomes and inferred ancestors. This approach reduces index size by up to 600-fold and construction time by over three orders of magnitude relative to existing tools. Panmap places a 100× coverage SARS-CoV-2 sample onto 20,000 genomes in 0.4 seconds and onto 8 million genomes in under two minutes. Furthermore, it enables accurate haplotype identification and abundance estimation in metagenomic samples and sensitive placement of ancient environmental DNA without prior alignment. Our approach makes large-scale pangenomes directly amenable to read mapping, genome assembly, alignment-free phylogenetic placement, and metagenomic analysis.},
}

@article {pmid41959403,
year = {2026},
author = {Maier, J and Gin, C and Rabasco, J and Spencer, W and Bass, A and Duerkop, BA and Callahan, B and Kleiner, M},
title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715651},
pmid = {41959403},
issn = {2692-8205},
abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.

RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.

CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.},
}

@article {pmid41959459,
year = {2026},
author = {Kim, M and Ardell, SM and Kryazhimskiy, S},
title = {Module-Selection Balance in the Evolution of Modular Organisms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.01.715873},
pmid = {41959459},
issn = {2692-8205},
abstract = {The architecture of the genotype-phenotype-fitness map (GPFM) is a key determinant of evolutionary dynamics. One salient feature of biological GPFMs is variational modularity, where each mutation affects only a small subset of functional traits. Variational modularity may constrain the dynamics of trait evolution, but these constraints are not well understood. Here, we use several extensions of the Fisher's geometric model with two functional traits to investigate these constrains. We find that on GPFMs with universal pleiotropy, populations evolve along the fitness gradient, which implies that the trait under stronger selection is optimized exponentially faster than the trait under weaker selection. In contrast, on modular GPFMs, populations approach a quasi-steady state that we term a "module-selection balance" where both traits improve at the same rate and their ratio remains constant. We demonstrate that the existence of a module-selection balance is robust with respect to the details of evolutionary dynamics and GPFMs themselves, as long as they are variationally modular. Our theory predicts that variationally modular organisms should exhibit stereotypical bi-phasic dynamics of genome evolution, especially in the strong clonal interference regime, and we find support for this prediction in metagenomic data from Lenski's long-term evolution experiment in bacterium Escherichia coli . We propose that module-selection balance is an inherent feature of variationally modular GPFMs, which imposes an important constraint on long-term trait evolution.},
}

@article {pmid41959466,
year = {2026},
author = {Sapoval, N and Treangen, TJ and Nakhleh, L},
title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.10.710879},
pmid = {41959466},
issn = {2692-8205},
abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.

RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.

https://github.com/nsapoval/bd-gsl.},
}

@article {pmid41959535,
year = {2026},
author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG},
title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715631},
pmid = {41959535},
issn = {2692-8205},
abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.},
}

@article {pmid41959658,
year = {2026},
author = {Funauchi, A and Hashimoto, K and Fukushima, K and Matsumoto, Y and Hamada, N and Hara, R and Niitsu, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H},
title = {Gastric Aspirate Isolate Demonstrates Strain-Level Concordance With Sputum Isolate in Nontuberculous Mycobacterial Pulmonary Disease.},
journal = {Open forum infectious diseases},
volume = {13},
number = {4},
pages = {ofag175},
pmid = {41959658},
issn = {2328-8957},
abstract = {The nontuberculous mycobacteria (NTM) isolated from gastric aspirate have demonstrated >85% strain concordance with those from the sputum, suggesting that they originate from the lungs rather than the environment. Gastric aspirate, although not yet internationally recognized, may be a useful supplementary specimen for diagnosing NTM pulmonary disease.},
}

@article {pmid41960427,
year = {2026},
author = {Nuanmuang, N and Leekitcharoenphon, P and Njage, PMK and Jirakkakul, J and Dulsawat, S and Tachaleat, A and Svendsen, CA and Møller, FD and Otani, S and Cheevadhanarak, S and Aarestrup, FM},
title = {Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790551},
pmid = {41960427},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a significant public health threat and is associated with millions of deaths worldwide each year. Besides antimicrobial usage, different socioeconomic factors have recently gained attention as being associated with increased AMR. Bangkok, a city with diverse income levels, provided a unique setting for this study, which aimed to explore the possible within-city association between income-level areas and the diversity and abundance of AMR. Twenty-seven toilet waste samples were collected from nine different sites (low-, middle-, and high-income) during March-April 2023, and metagenomic sequencing was performed. The sequencing data were quality checked, and sequences that passed quality control were mapped to antimicrobial, metal, and disinfectant resistance gene databases as well as bacterial taxonomy databases. We observed higher antibiotic resistance genes (ARGs), metal resistance, and disinfectant resistance abundance (fragments per kilobase per million mapped reads, FPKM) in low-income groups compared to middle- and high-income groups. This included both acquired ARGs and presumed intrinsic ARGs, including genes associated with completely novel antibiotics that have so far only been identified through functional cloning. Significant differences in individual ARGs were also observed between sites. Our study highlights the relative abundance of ARGs across different income groups, emphasizing how the development of resistance mechanisms revealed through metagenomic analysis can serve as a valuable tool for city-level surveillance of AMR from toilet waste, particularly in low-income settings.},
}

@article {pmid41960429,
year = {2026},
author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL},
title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1691133},
pmid = {41960429},
issn = {1664-302X},
abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.

METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.

RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.

DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.},
}

@article {pmid41960438,
year = {2026},
author = {Zhao, Z and Xiang, L and Liu, Y and Xu, S and Chen, Y and Yu, M},
title = {Rare fungal keratitis caused by plant pathogens: report of two cases and review of the literature.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1785252},
pmid = {41960438},
issn = {2673-6128},
abstract = {Macrophomina phaseolina and Colletotrichum fructicola are notable plant pathogens, yet cases of keratitis from these fungi are rarely reported. Limited awareness of this keratitis etiology among ophthalmic professionals reduces the likelihood of accurate diagnosis and timely treatment. This report aims to improve the understanding of these rare infections in eye care. We present two cases of keratitis: one caused by M. phaseolina and another by C. fructicola, both of whom experienced a complicated treatment course. Traditional fungal exams yielded negative results, which limited disease identification and focused therapy. To determine the cause, we used metagenomic next-generation sequencing (mNGS) on clinical samples obtained from corneal scrapings. The mNGS report was received during therapy and quickly identified the pathogen. Based on this, we looked for treatment regimens for this kind of infection in previous literature, altered and implemented appropriate antifungal drug therapy, and the patient's condition improved. We review the literature from 1970 to 2025 on M. phaseolina and Colletotrichum spp. keratitis. We identified 10 cases of M. phaseolina keratitis from four studies and 72 cases of Colletotrichum spp. keratitis, including five of C. fructicola, in 43 articles. Misdiagnosis was common due to limited clinical and microbiologic suspicion. The rise of infections by rare pathogens highlights diagnostic challenges. Traditional methods often delay accurate diagnosis, while mNGS enables rapid identification of pathogen, crucial for effective treatment and vision preservation.},
}

@article {pmid41960830,
year = {2026},
author = {Sun, S and Zhou, Y and Deng, F and Meng, Y and Zhu, X and Wang, H and Wei, D},
title = {Engineering an l-Threonine Aldolase from Staphylococcus epidermidis for Enhanced Diastereoselectivity in the Synthesis of a Chloramphenicol Intermediate.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01578},
pmid = {41960830},
issn = {1520-5118},
abstract = {l-Threonine aldolase (LTA) is an attractive biocatalyst for the synthesis of l-syn-p-nitrophenylserine (l-syn-1b), a key intermediate in chloramphenicol synthesis. However, low diastereoselectivity has limited its broader application in stereospecific C-C bond formation. To overcome this limitation, a metagenomic library constructed from non-natural amino acid-enriched environments was screened, leading to the identification of an LTA from Staphylococcus epidermidis (SeLTA) that exhibits the highest diastereoselectivity toward l-syn-1b among naturally occurring LTAs reported to date. To further enhance its diastereoselectivity, structural comparison, alanine scanning, and tunnel analysis were employed to identify hotspots that modulate the diastereoselectivity of SeLTA. Subsequent saturation mutagenesis and iterative saturation mutagenesis at these positions yielded the quadruple variant A176G/Y202S/N7C/F129E (Mut4), which increased the diastereoselectivity from 32.5%syn to 92.7%syn. Furthermore, Mut4 exhibits markedly improved diastereoselectivity toward para- and meta-substituted benzaldehyde derivatives. Molecular dynamics (MD) simulations further elucidated the molecular basis underlying the enhanced diastereoselectivity of Mut4. This study provides a potential biocatalyst for the sustainable and efficient synthesis of a chloramphenicol intermediate.},
}

@article {pmid41961352,
year = {2026},
author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H},
title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.},
journal = {Neurochemical research},
volume = {51},
number = {2},
pages = {},
pmid = {41961352},
issn = {1573-6903},
}

@article {pmid41961522,
year = {2026},
author = {Song, W and Li, M and Yue, X and Meng, Y and Xie, Y and Zhang, Y and Hu, Y and Zheng, Y and Yue, X},
title = {Microbial succession and metabolic mechanisms driving flavor evolution in Northeast Chinese dajiang: a comprehensive review integrating insights from East Asian fermented soybean pastes.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/10408398.2026.2644602},
pmid = {41961522},
issn = {1549-7852},
abstract = {This review systematically explores the spatiotemporal microbial succession and flavor evolution during the fermentation of northeast Chinese soybean paste (dajiang), with a focus on the jiangpei (solid-state starter) and jianglao (brine fermentation) stages. By integrating metagenomic, metabolomic, and sensory data, this review synthesizes evidence linking microbial community dynamics-featuring Lactobacillus spp., Zygosaccharomyces rouxii, and Aspergillus oryzae-to the biosynthesis of key flavor compounds. These include umami amino acids (e.g., glutamic acid, 1.5-2.0 g/kg), fruity esters (e.g., ethyl acetate, 124.67 μg/kg), and phenolic antioxidants. Cross-feeding interactions (e.g., yeast utilization of lactic acid for ester synthesis) and environmental stressors (12%-18% NaCl, 25 °C-30 °C) are shown to enhance flavor complexity by modulating metabolic pathways like amino acid degradation and lipid β-oxidation. Unlike prior studies focusing on fragmented fermentation stages, this review systematically addresses the full fermentation continuum, highlighting how aerobic-to-anaerobic transitions drive functional metabolite accumulation. The review concludes by outlining a roadmap to modernize dajiang production through standardized quality control, precision flavor modulation, and traditional process optimization, enabled by culturomics/MAGs, multi-omics integration, and AI-assisted fermentation monitoring and control.},
}

@article {pmid41961886,
year = {2026},
author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T},
title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345919},
doi = {10.1371/journal.pone.0345919},
pmid = {41961886},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; },
abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.},
}

Humans
*Metagenomics/methods
Machine Learning
*Gastrointestinal Microbiome/genetics
*Microbiota
Inflammatory Bowel Diseases/microbiology
Neural Networks, Computer
Multiomics

@article {pmid41962241,
year = {2026},
author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S},
title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.},
journal = {Water research},
volume = {299},
number = {},
pages = {125879},
doi = {10.1016/j.watres.2026.125879},
pmid = {41962241},
issn = {1879-2448},
abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.},
}

@article {pmid41962374,
year = {2026},
author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ},
title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141891},
doi = {10.1016/j.jhazmat.2026.141891},
pmid = {41962374},
issn = {1873-3336},
abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.},
}

@article {pmid41963033,
year = {2026},
author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I},
title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105049},
doi = {10.1016/j.fm.2026.105049},
pmid = {41963033},
issn = {1095-9998},
mesh = {*Cheese/microbiology/classification/analysis ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Animals ; Milk/microbiology ; Phylogeny ; Greece ; },
abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.},
}

*Cheese/microbiology/classification/analysis
*Microbiota
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Food Microbiology
High-Throughput Nucleotide Sequencing
Animals
Milk/microbiology
Phylogeny
Greece

@article {pmid41963036,
year = {2026},
author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y},
title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105055},
doi = {10.1016/j.fm.2026.105055},
pmid = {41963036},
issn = {1095-9998},
mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.},
}

*Oryza/microbiology/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
Phylogeny
Metagenomics
Anti-Bacterial Agents/pharmacology
Soil Microbiology
Seeds/microbiology
Microbiota
Metagenome
*Genes, Bacterial
*Drug Resistance, Microbial/genetics

@article {pmid41963043,
year = {2026},
author = {Liu, G and Zhong, J and Yang, D and Zeng, Y and Cao, R and He, S and Bai, W and Qu, C},
title = {The mechanisms underlying ester enhancement and higher alcohol reduction in Chi-flavor base liquor brewing via Limosilactobacillus fermentum fortification: A multi-omics investigation.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105070},
doi = {10.1016/j.fm.2026.105070},
pmid = {41963043},
issn = {1095-9998},
mesh = {Fermentation ; *Limosilactobacillus fermentum/metabolism/genetics/isolation & purification ; *Alcoholic Beverages/microbiology/analysis ; *Esters/metabolism/analysis ; *Flavoring Agents/metabolism/analysis ; Saccharomyces cerevisiae/metabolism/genetics ; Acetates/metabolism/analysis ; *Alcohols/metabolism/analysis ; Ethanol/metabolism/analysis ; Lactates/metabolism/analysis ; Taste ; Bacteria/genetics/classification/isolation & purification/metabolism ; Multiomics ; },
abstract = {Chi-flavor Baijiu is a unique liquor in the Pearl River Delta region. Ethyl lactate is the key flavor with low content in base liquor, affecting qualities of Chi-flavor Baijiu. To address this issue, Limosilactobacillus fermentum Y8 (Y8) isolated from sour mash, was used to fortify the fermentation. Results showed that contents of ethyl acetate and ethyl lactate reached to 663.55 mg/L and 604.25 mg/L, increased by 334.97% and 331.26%, respectively, with that of ethanol unchanged and main higher alcohols reduced significantly. Metagenomic analysis revealed that Lactiplantibacillus, Limosilactobacillus, Pediococcus, Levilactobacillus, and Lactobacillus were the top five abundance species. Metatranscriptomic data indicated that Saccharomyces cerevisiae, Lactobacillus brevis and L. fermentum were the dominant active species, the succession of which was significantly influenced by Y8 addition. Correlation analysis revealed that L. fermentum was positively related to reducing sugar, total acid and esters, while negatively to higher alcohols. Based on metatranscriptomic analysis, a new pathway for lactate synthesis from lactaldehyde was found with Y8 fortification, along with acyl-CoA thioester hydrolase gene ybgC upregulated significantly, providing more precursors for ester synthesis. At the same time, enzymes related to ester synthesis were upregulated with that of higher alcohols downregulated. Collectively, Y8 fortification could affect the succession of microbiota and promote the synthesis of ester precursors and ester synthesis pathway, and decrease higher alcohols synthesis pathway. This study not only provides a strain to fortify Chi-Flavor Baijiu brewing with improved qualities but also reveals mechanisms of flavor modulation and microbial community succession during the brewing process.},
}

Fermentation
*Limosilactobacillus fermentum/metabolism/genetics/isolation & purification
*Alcoholic Beverages/microbiology/analysis
*Esters/metabolism/analysis
*Flavoring Agents/metabolism/analysis
Saccharomyces cerevisiae/metabolism/genetics
Acetates/metabolism/analysis
*Alcohols/metabolism/analysis
Ethanol/metabolism/analysis
Lactates/metabolism/analysis
Taste
Bacteria/genetics/classification/isolation & purification/metabolism
Multiomics

@article {pmid41963048,
year = {2026},
author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M},
title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105075},
doi = {10.1016/j.fm.2026.105075},
pmid = {41963048},
issn = {1095-9998},
mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; },
abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.},
}

Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Animals
Swine
Food Storage
*Meat Products/microbiology/analysis
Cooking
*Microbiota
Food Microbiology
Food Handling

@article {pmid41963049,
year = {2026},
author = {Zhai, WT and Zhao, H and Chai, LJ and Zhang, W and Zhang, XJ and Lu, ZM and Gao, CQ and Si, GR and Zhang, WQ and Wang, ST and Shen, CH and Xu, ZH},
title = {Microbial and environmental determinants of 1-propanol biosynthesis in Jiang-flavor Baijiu fermentation.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105076},
doi = {10.1016/j.fm.2026.105076},
pmid = {41963049},
issn = {1095-9998},
mesh = {Fermentation ; *Flavoring Agents/metabolism ; *1-Propanol/metabolism ; *Wine/microbiology/analysis ; *Yeasts/metabolism/genetics/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Saccharomyces cerevisiae/metabolism ; Hydrogen-Ion Concentration ; },
abstract = {1-Propanol is a crucial flavor compound in Jiang-flavor Baijiu, yet the key microbial pathways and environmental factors controlling its synthesis have not been systematically investigated. Using an integrated approach of metagenomics and culture-dependent techniques, this study identified the key microbes, pathways, and factors controlling 1-propanol synthesis. The highest 1-propanol level was detected in first-round base Baijiu, with rapid accumulation during early pit fermentation. Metagenomics revealed the propanoate pathway as the dominant route, primarily contributed by Limosilactobacillus, while Pichia and Saccharomyces were key providers of pyruvate decarboxylase in the citramalate and threonine pathways. Pure-culture validation confirmed that L. panis MR32 predominantly utilizes 1,2-propanediol as the precursor, while yeasts such as P. kudriavzevii 2J2 and S. cerevisiae LB7A prefer the 2-ketobutyrate pathway. Environmental tests revealed optimal 1-propanol production by L. panis MR32 at pH 5.5 and increasing yields with temperature (25-45 °C). In contrast, most yeasts produced the most 1-propanol at 30 °C, beyond which yields declined, with only P. kudriavzevii 2J2 and I. orientalis IO tolerating high lactic acid. Our findings clarify the microbial division of labor and environmental drivers of 1-propanol formation, enabling targeted fermentation control.},
}

Fermentation
*Flavoring Agents/metabolism
*1-Propanol/metabolism
*Wine/microbiology/analysis
*Yeasts/metabolism/genetics/classification/isolation & purification
*Bacteria/metabolism/genetics/classification/isolation & purification
Temperature
Metagenomics
Saccharomyces cerevisiae/metabolism
Hydrogen-Ion Concentration

@article {pmid41963512,
year = {2026},
author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y},
title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47830-x},
pmid = {41963512},
issn = {2045-2322},
abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.},
}

@article {pmid41963805,
year = {2026},
author = {Roslan, MF and Saad, MFM and Pau, SSN and Basir, S and Aziz, H and Akbar, MA and Bunawan, H},
title = {Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01422-w},
pmid = {41963805},
issn = {2730-6844},
}

@article {pmid41963968,
year = {2026},
author = {Zhou, N and Liu, J and Zhang, X and Xiao, G and Zhang, M},
title = {Vitamin K2 emerges as the key mediator: Cetobacterium somerae ZNN-1 increases muscle protein deposition and improves liver health in Nile tilapia (Oreochromis niloticus).},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41963968},
issn = {1674-9782},
support = {32373145//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Cetobacterium somerae (C. somerae) is a common indigenous bacterium in the intestine of freshwater fish. Studies have shown that it has the potential to promote protein deposition, but the underlying mechanisms remain unclear.

RESULTS: Nile tilapia were fed with C. somerae ZNN-1 (10[8] CFU/g feed), which significantly increased the carcass ratio, reduced the hepatosomatic index, and decreased whole-body lipid content. Supplementation of C. somerae ZNN-1 significantly increased the crude protein content in muscle, promoted glucose uptake and utilization in muscle tissue, and activated the phosphorylation of S6K/S6 in muscle tissue. C. somerae ZNN-1 supplementation significantly decreased hepatic total lipid, triglyceride, and free fatty acid contents. Further analysis revealed that C. somerae ZNN-1 supplementation markedly activated the phosphorylation of hepatic AMPK and upregulated the expression of genes involved in hepatic lipolysis and fatty acid β-oxidation. Integrated serum metabolomic, bacterial genomic, and gut metagenomic analyses revealed that C. somerae ZNN-1 synthesized chorismate (CHA), which serves as a precursor for gut microbiota to produce vitamin K2 (VK2). In vitro experiments demonstrated that VK2 activated the S6K/S6 pathway to promote protein synthesis, while stimulating AMPK phosphorylation and activating lipid catabolism to reduce fat accumulation.

CONCLUSIONS: These findings provide a theoretical basis for the application of C. somerae ZNN-1 in enhancing edible protein content and reducing fat deposition of aquatic animals.},
}

@article {pmid41964024,
year = {2026},
author = {Sosef, NP and Boxman, ILA and Dirks, RAM},
title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03159-5},
pmid = {41964024},
issn = {1743-422X},
support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; },
abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.},
}

@article {pmid41964077,
year = {2026},
author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ},
title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02395-9},
pmid = {41964077},
issn = {2049-2618},
support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; },
abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.

RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.

CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.},
}

@article {pmid41964107,
year = {2026},
author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W},
title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2657047},
doi = {10.1080/19490976.2026.2657047},
pmid = {41964107},
issn = {1949-0984},
abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.},
}

@article {pmid41764595,
year = {2026},
author = {Martínez-Murcia, A and Navarro, A and Miró-Pina, C and García-Sirera, A and Pérez, L and García-Román, V and Navarro-Gracia, JF},
title = {Early detection of nosocomial pathogens in air and surfaces using an innovative genetic approach for surveillance in healthcare settings.},
journal = {Antimicrobial resistance and infection control},
volume = {15},
number = {1},
pages = {},
pmid = {41764595},
issn = {2047-2994},
support = {INNCAD/2022/23//AVI/ ; },
abstract = {BACKGROUND: Healthcare-associated infections remain a major cause of morbidity, mortality, and financial burden worldwide, further exacerbated by the emergence of antimicrobial resistance. Environmental reservoirs of pathogens, including air and surfaces, play a critical role in nosocomial transmission. This study aimed to validate an integrated air and surface molecular surveillance system for the early detection of clinically relevant pathogens and resistance genes in hospital environments.

METHODS: Weekly air and surface samples were collected over 28 weeks from two hospitals in southeastern Spain. DNA and RNA were extracted and analysed by quantitative PCR (qPCR) targeting bacterial, fungal, and viral pathogens, as well as antimicrobial resistance genes. A subset of samples underwent shotgun metagenomic sequencing to confirm qPCR results and characterize microbial communities. Environmental findings were compared with clinical infection data from both hospitals.

RESULTS: Viral, bacterial and fungal pathogens were detected with similar patterns between air and surface samples and between hospitals. Carbapenem resistance genes showed distinct distribution profiles between hospitals. Respiratory viruses displayed strong temporal correlations with patient admissions, with viral RNA occasionally detected before clinical peaks.

CONCLUSIONS: This integrated molecular surveillance system allows sensitive detection of pathogens and resistance genes in hospital environments. Coupling air and surface sampling with qPCR provides a robust tool for identifying contamination sources and tracking temporal infection trends. Its scalability and adaptability make it suitable for implementation as an early warning system in infection prevention programmes, enhancing patient safety and supporting proactive control of nosocomial infections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13756-026-01725-8.},
}

@article {pmid41771971,
year = {2026},
author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J},
title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41771971},
issn = {2045-2322},
support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; },
abstract = {UNLABELLED: Ganoderma lucidum has a long-standing history of use as a medicinal mushroom, with its spore oil (GLSO) extracted from broken cell walls using CO2 supercritical extraction. However, there is a notable scarcity of experimental studies on the protective effects and underlying mechanisms of GLSO on immune function impairment. The present study aims to explore the characteristics that GLSO contributes to protecting immune functions in cyclophosphamide-induced immunocompromised mice through a multi-omics analysis approach. GLSO administration significantly improved serum hemolysin levels, macrophage phagocytosis, and NK cell activity in immunosuppressed mice. Metagenomics, metabolomic, and proteomic analyses revealed that the immune protection mediated by GLSO was associated with structural rearrangements within gut microflora and shifts in microbial diversity. Specifically, there was an increase in beneficial microorganisms and a decrease in pathogenic organisms, accompanied by various alterations in metabolites and protein expressions. The identified 5 metabolites (propionic acid, beta-glycyrrhetinic acid, 3-aminosalicylic acid, creatine, and 2-phenylacetamide) and 5 proteins (Slc9a9, Blm, Hk3, AP1M2, and J chain) might serve as potential mediators of GLSO to alleviate immune dysfunction collectively caused by CYP in immunosuppressed mice.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40137-x.},
}

@article {pmid41935036,
year = {2026},
author = {Larsson, DGJ and Flach, CF and Kristiansson, E},
title = {Antibiotic resistance gene analyses in microbial communities: challenges and opportunities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41935036},
issn = {2041-1723},
support = {2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain.},
}

@article {pmid41952168,
year = {2026},
author = {Shen, Y and Qu, S},
title = {Ganciclovir for severe neonatal varicella pneumonia when acyclovir is unavailable: a case report.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03142-0},
pmid = {41952168},
issn = {1743-422X},
abstract = {BACKGROUND: Perinatal varicella is a rare and severe condition with a high mortality rate, particularly when it leads to complications such as pneumonia in neonates. Acyclovir is the standard treatment for varicella-zoster virus (VZV) infections; however, limited options exist when it is unavailable. This case report describes the successful treatment of neonatal varicella pneumonia with ganciclovir and provides insights into its potential as an alternative therapy. A female Asian neonate was admitted to our hospital on the 9th day of life with a rash, fever, and respiratory distress. Her mother developed varicella at 39 weeks of pregnancy, four days before delivery. The infant was diagnosed with VZV pneumonia based on clinical presentation and confirmed by detection of VZV DNA in blood(metagenomic next-generation sequencing detected 109,491 sequences with 100% relative abundance and 99% confidence).

INTERVENTION: Ganciclovir 5 mg/kg every 12 h for 8 days; intravenous immunoglobulin 400 mg/kg once daily for 3 days.

OUTCOME: The infant was successfully weaned off mechanical ventilation, with normalized blood gas parameters (PaO₂/FiO₂ ratio 346) and inflammatory markers (CRP decreased from 29.44 mg/L to 2.87 mg/L). She was discharged home with stable breathing and crusted skin lesions. Telephone follow-up at 2 and 4 weeks post-discharge confirmed the infant remained well with no respiratory symptoms or developmental concerns.

CONCLUSION: Ganciclovir may serve as a life-saving alternative for severe neonatal VZV pneumonia when acyclovir is unavailable. This case highlights the need for further research to establish its safety, optimal dosing, and efficacy in this population.},
}

@article {pmid41953110,
year = {2026},
author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J},
title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101380},
pmid = {41953110},
issn = {2352-7714},
abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.},
}

@article {pmid41953529,
year = {2026},
author = {Brown, JR and Ross, CS and Worth, A and Merve, A and Storey, N and Hacohen, Y and Mankad, K and Kaliakatsos, M and Shendi, HM and Atkinson, L and Gilmour, K and Hatcher, J and Lennon, A and Bamford, A and Kusters, M and Elfeky, R and Núñe, A and Brown, IH and Reid, SM and Cooper, J and Byrne, AMP and James, J and Lean, FZ and Banyard, AC and Breuer, J},
title = {Identifying virulent avian paramyxovirus type-1: A paediatric case of progressive encephalitis diagnosed by clinical metagenomics with case series review.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02555},
pmid = {41953529},
issn = {2214-2509},
abstract = {BACKGROUND: Immunocompromised patients presenting with encephalitis can present a diagnostic conundrum as infection can be caused by a broad range of pathogens, many of which are not detected by standard of care testing pathways. Untargeted metagenomics has proven utility in the diagnosis of such infections, particularly for immunocompromised patients.

METHODS: An immunosuppressed adolescent presented with idiopathic progressive muscle weakness resulting in respiratory failure, 16 years after haematopoeitic stem cell transplant for familial haemophagocytic lymphohistiocytosis type 5. Clinical and radiological findings suggested a diagnosis of isolated central nervous system haemophagocytic lymphohistiocytosis, however the patient demonstrated no improvement on immunosuppressive therapy. Untargeted metagenomics was performed on brain biopsy tissue.

RESULTS: Clinical metagenomics detected avian paramyxovirus 1 (APMV-1) in the brain tissue 12 days after biopsy, confirmed by targeted PCR and immunohistochemistry. The metagenomics results guided treatment; immunosuppression was stopped and medication with potential activity against RNA viruses started. The patient died 8 months after symptom onset.

CONCLUSIONS: We describe the third published case of fatal encephalitis caused by APMV-1, detectable only in brain parenchyma and only by clinical metagenomics, demonstrating the utility of brain biopsy and metagenomics when investigating encephalitis in immunocompromised patients. Case series review suggests profoundly immunocompromised patients are at risk of severe infection caused by AMPV-1.},
}

@article {pmid41953658,
year = {2026},
author = {Song, J and Li, Y and Wang, L and Zhang, J and Shi, C and Zhong, L and Liu, C and Song, M and Yu, X and Zhang, W and Wen, P},
title = {Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103771},
pmid = {41953658},
issn = {2590-1575},
abstract = {This study aimed to elucidate differences between the commercial starter culture (CK) and traditional starters from different Tibetan regions (Gannan (GN), Qinghai (QH), Tibet (XZ)) in fermenting yak yogurt by physicochemical properties, flavor, and bacterial community. Results indicated acidity, proline, arginine, alanine, and C6:0 contents were significantly higher in the traditional starter culture than CK (P < 0.05). Gas chromatography-ion mobility spectrometry analysis found the traditional starter culture group was dominated by alcohols and esters, whereas CK exhibited richer ketones. Metagenomic analysis revealed Lactobacillus delbrueckii (49.56% in XZ, 24.86% in GN) and Streptococcus spp. (18.30% in CK, 17.21% in QH) as the dominant. Moreover, pH and titratable acidity were primary factors affecting microbial diversity. Meanwhile, glutamic acid modulated ester biosynthesis like ethyl acetate, while C16:0 fatty acids inhibited off-odor ketones such as 2-pentanone. This study offers valuable insights into developing specialized fermentation agents and standardizing the quality of yak yogurt.},
}

@article {pmid41953764,
year = {2026},
author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF},
title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41953764},
issn = {2312-0541},
abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.

METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.

RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in α- and β-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.

CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.},
}

@article {pmid41954112,
year = {2026},
author = {Banerjee, M and Lahiri, A and Basak, S and DAS, S and Mukhopadhyay, S and Banerjee, R and Basak, K},
title = {StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.},
journal = {Journal of biosciences},
volume = {51},
number = {},
pages = {},
pmid = {41954112},
issn = {0973-7138},
mesh = {Humans ; Algorithms ; *Cross Infection/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; Autoencoder ; },
abstract = {As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for Enterococcus faecium using 4-mer data, with similar results for other organisms using various k-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.},
}

Humans
Algorithms
*Cross Infection/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Drug Resistance, Bacterial/genetics
Computational Biology/methods
Autoencoder

@article {pmid41954388,
year = {2026},
author = {Zhao, P and Liu, H and Dong, J and Su, H and Jin, Q and Yang, F},
title = {From hepatitis misdiagnosis to zoonotic false alarms: a metagenomic blacklist framework for the parvo-like hybrid viral group.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0015726},
doi = {10.1128/spectrum.00157-26},
pmid = {41954388},
issn = {2165-0497},
}

@article {pmid41954393,
year = {2026},
author = {Shukla, N and Budhbhatti, U and Puvar, A and Raval, I and Pandit, R and Chavda, P and Chauhan, A and Jhala, D and Shah, D and Shah, T and Raval, J and Prajapati, H and Patel, N and Upadhyay, K and Joshi, M and Patel, AK and Bondre, V and Kumar, N and Joshi, C},
title = {Genomic and evolutionary characterization of Chandipura virus: a cause of the 2024 outbreak in Gujarat, India.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0157825},
doi = {10.1128/spectrum.01578-25},
pmid = {41954393},
issn = {2165-0497},
abstract = {UNLABELLED: Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its transmission dynamics and evolutionary behavior. CHPV is endemic in India, with previous outbreaks (2003-2004) reported case fatality rates (CFRs) ranging from 56% to 75%. In the current (2024) outbreak, the CFR declined to 46%, with an overall test-positivity rate of 18.6%, possibly reflecting improvements in supportive care. Despite advances in genomics and sequencing technologies, only a limited number of CHPV genomes are publicly available. To address this gap, we performed whole-genome sequencing of CHPV isolated from a pediatric patient aged 12 years from Patan, Gujarat. Comparative genomic analysis with previously reported Indian strain revealed approximately 293 mutations, including 24 non-synonymous. The estimated evolutionary rate of CHPV was ~1.62 × 10[-2] substitutions/site/year. Furthermore, the selective pressure analysis showed that, despite the virus being under strong purifying (negative) selection, several non-synonymous changes were identified. Nonetheless, as the present analysis is based on the single genome, further sequencing, validation, and broader comparative analysis are required to draw a definitive inference. However, these findings suggest that even under purifying selection pressure, CHPV retains the ability to infect and cause severe disease in children. This highlights the continued need to investigate virus-host interactions, particularly host immune responses, to better understand CHPV pathogenesis and its ability to cause disease in children.

IMPORTANCE: Chandipura virus (CHPV) is an etiological agent of acute encephalitis syndrome (AES) in children, characterized by rapid neurological decline; yet the viral and host factors governing its neuropathogenesis and sudden outbreak dynamics remain poorly defined. Despite minimal genomic variation indicative of strong purifying selection, which supports the continued efficacy of existing molecular diagnostics and candidate therapeutics, CHPV re-emerges unpredictably in human populations, as exemplified by the 2024 AES cluster in Gujarat. This outbreak underscores the importance of continuous genomic surveillance to elucidate viral behavior and immune-evasion mechanisms. Moreover, it highlights the utility of both amplicon-based and metagenomic next-generation sequencing approaches for future CHPV detection and comprehensive genome characterization.},
}

@article {pmid41954722,
year = {2026},
author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C},
title = {Correction: Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next‑generation sequencing.},
journal = {Infection},
volume = {},
number = {},
pages = {},
doi = {10.1007/s15010-026-02771-5},
pmid = {41954722},
issn = {1439-0973},
}

@article {pmid41954798,
year = {2026},
author = {Liu, P and Zhang, J and Liu, X and Li, B and Peng, Y and Li, B and Lyu, X and Tan, L and Guo, Z and Li, Z and Hu, M},
title = {Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41954798},
issn = {1435-4373},
support = {Grant No.2023XQLH173//Central Universities of Central South University/ ; No. 82102499//National Natural Science Foundation of China/ ; No. 82270658//National Natural Science Foundation of China/ ; No. 2021JJ40840//the Hunan Natural Science Foundation/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; },
}

@article {pmid41954996,
year = {2026},
author = {Prabhu, A and Rinke, C},
title = {ICTV Virus Taxonomy Profile: Krittikaviridae 2026.},
journal = {The Journal of general virology},
volume = {107},
number = {4},
pages = {},
doi = {10.1099/jgv.0.002239},
pmid = {41954996},
issn = {1465-2099},
mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Virion/ultrastructure/genetics ; DNA, Viral/genetics ; *Archaea/virology ; Virus Replication ; },
abstract = {The family Krittikaviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. These viruses have been identified through metagenomic analysis of brackish estuarine samples and are closely related to other 'magroviruses'. The family belongs to the order Magrovirales and includes the genus Velanvirus and the species Velanvirus brisbanense. Viruses in the family have a genome of about 80 kbp that includes modules for DNA replication and virion morphogenesis. Krittikavirids are predicted to form virions with an icosahedral capsid and helical tail, characteristic of viruses belonging to the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Krittikaviridae, which is available at ictv.global/report/krittikaviridae.},
}

Genome, Viral
Phylogeny
*DNA Viruses/classification/genetics/ultrastructure/isolation & purification
Virion/ultrastructure/genetics
DNA, Viral/genetics
*Archaea/virology
Virus Replication

@article {pmid41955630,
year = {2026},
author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H},
title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/23744235.2026.2654559},
pmid = {41955630},
issn = {2374-4243},
abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.

METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.

RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n = 18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.

CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.},
}

@article {pmid41955710,
year = {2026},
author = {Sahu, TK and Rathored, J and Patil, P},
title = {Tri-layer microbiology for LMIC Hospitals: linking syndromic panels with reflex culture and targeted sequencing for real world care - a narrative review.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {30},
number = {3},
pages = {105808},
doi = {10.1016/j.bjid.2026.105808},
pmid = {41955710},
issn = {1678-4391},
abstract = {Rapid, syndromic molecular panels and high throughput sequencing have transformed the diagnostic landscape for sepsis, respiratory, gastrointestinal, and central nervous system infections, but their value in routine practice depends on how they are integrated with conventional microbiology and antimicrobial stewardship. This review synthesises recent high-quality evidence to propose a pragmatic three-tier hybrid framework. Tier 1 comprises syndrome specific rapid panels that provide organism and selected resistance markers within hours, primarily to accelerate early escalation or de-escalation rather than to replace culture. Tier 2 positions reflex culture and targeted adjunct tests as the non-negotiable specificity anchor, confirming molecular hits, distinguishing infection from colonisation or contamination, generating phenotypic susceptibility data and supplying isolates for infection prevention and public health surveillance. Tier 3 reserves targeted or metagenomic sequencing for a small, clinically critical subset of high suspicion, panel negative and culture negative cases, where additional breadth can realistically change management. Across sepsis/BSI, pneumonia, gastrointestinal infection and CNS disease, available data indicate that clinical benefit is driven less by any individual technology and more by disciplined implementation: clear indications, explicit reflex rules, close linkage to antimicrobial stewardship and systematic audit of key performance indicators such as time-to-targeted therapy, spectrum of antimicrobial use and cost per additional actionable diagnosis. The proposed tiered, syndrome wise algorithms provide a transferable conceptual scaffold that can be adapted to local resources, allowing laboratories in both high and low resource settings to introduce advanced diagnostics without abandoning culture-based anchors or stewardship accountability.},
}

@article {pmid41955799,
year = {2026},
author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G},
title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141956},
doi = {10.1016/j.jhazmat.2026.141956},
pmid = {41955799},
issn = {1873-3336},
abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.},
}

@article {pmid41955854,
year = {2026},
author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H},
title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128089},
doi = {10.1016/j.envpol.2026.128089},
pmid = {41955854},
issn = {1873-6424},
abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.},
}

@article {pmid41955934,
year = {2026},
author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM},
title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.},
journal = {The Science of the total environment},
volume = {1030},
number = {},
pages = {181776},
doi = {10.1016/j.scitotenv.2026.181776},
pmid = {41955934},
issn = {1879-1026},
abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.

METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.

RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.

CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.},
}

@article {pmid41955982,
year = {2026},
author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D},
title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.},
journal = {Water research},
volume = {299},
number = {},
pages = {125876},
doi = {10.1016/j.watres.2026.125876},
pmid = {41955982},
issn = {1879-2448},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.},
}

@article {pmid41955988,
year = {2026},
author = {Wang, X and Xue, T and Li, J and Zhang, C and Hao, G and Xing, Y and Tao, R and Guo, L and Zhang, H and Chai, S and Zheng, L},
title = {Novel photoelectron-driven nitrate reduction in anammox granules using photosensitive semiconductor iron mineral for wastewater treatment.},
journal = {Water research},
volume = {299},
number = {},
pages = {125862},
doi = {10.1016/j.watres.2026.125862},
pmid = {41955988},
issn = {1879-2448},
abstract = {The accumulation of nitrate byproducts and limited electron availability fundamentally constrain the efficacy of anaerobic ammonium oxidation (anammox) processes. While iron minerals regulate electron transfer, their potential to drive anammox via semiconductive photoexcitation remains underexplored. Here, we establish a novel "Photo-Chemo-Bio" strategy to overcome these thermodynamic bottlenecks using light-excited hematite (α-Fe2O3). Among tested minerals, hematite exhibited superior band-structure suitability, achieving a 3.65-fold photocurrent enhancement (4.06 μA·cm[-2]) upon bio-hybridization, facilitated by the active recruitment of photo-electrons via upregulated outer-membrane c-type cytochromes. Crucially, this photo-enhanced electron supply boosted the total nitrogen removal rate by 27.4% while suppressing nitrate yield by 42.8%. Kinetic analysis revealed a precise metabolic decoupling: solar irradiation did not accelerate ammonia oxidation but specifically diverted electron flow toward nitrate reduction pathways. Genome-resolved metagenomics unraveled the molecular basis of this synergy, identifying a "hardwired" cooperative network: flanking Desulfobacillus-like species, characterized by a specific metabolic truncation (absence of nor genes), act as obligate "net NO providers" to fuel the anammox core; concurrently, heterotrophic Casimicrobiaceae unexpectedly encode Photosystem II (psbA), functioning as auxiliary "energy antennas" to harvest photons. These findings demonstrate how mineral-microbe hybrids can orchestrate electron flux to close the nitrogen loop, offering a sustainable, carbon-free strategy for high-efficiency wastewater treatment.},
}

@article {pmid41956026,
year = {2026},
author = {Sorgato, AC and Kim, B and Papillon, J and Nivala, J and Silveira, DD and Lapolli, FR and Forquet, N},
title = {Microbial fuel cells inoculated with French vertical flow treatment wetland sludge: A step towards clogging biodetector development.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {171},
number = {},
pages = {109297},
doi = {10.1016/j.bioelechem.2026.109297},
pmid = {41956026},
issn = {1878-562X},
abstract = {Clogging is considered an operational challenge in French vertical flow treatment wetlands (VFTWs), causing hydraulics and aeration problems. The available monitoring methods are labor intensive. Microbial fuel cells (MFCs) have emerged as real-time biosensors, including for treatment wetlands (TW) systems. In this study, French VFTW sludge was investigated as inoculum in MFCs, to assessing its adaptation into electrochemical environment as a step for clogging MFC-based biodetector implementation in such systems. The results show that the inoculum was successfully adapted, with stable current generation at 0.4 mA. The electrochemical impedance spectroscopy (EIS) demonstrated the establishment of a biofilm with electroactive characteristics and non-limiting anode. Metagenomic analysis showed that the French VFTW harbor electroactive species, and the MFC created a selective pressure on the VFTW sludge inoculum and significantly shaped the microbial community and function, stimulating the enrichment of electroactive bacteria (EAB), such Geobacterales (4.11% to 5.83%), with potential expression of cytochrome-c for extracellular electron transference (EET). This study illustrates the feasibility of developing electroactive biofilms from French VFTW and suggests its use as an inoculum, improving the integration of TW-MFC systems. Considering these results, the well-adapted anodic biofilm could enable the detection of aeration limitations via cathodic reactions in future studies.},
}

@article {pmid41956515,
year = {2026},
author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH},
title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70300},
doi = {10.1111/1462-2920.70300},
pmid = {41956515},
issn = {1462-2920},
support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; },
mesh = {*Biofilms/growth & development ; *Ecosystem ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Cyanobacteria/genetics/classification ; Hydrology ; Droughts ; Floods ; Metagenomics ; },
abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.},
}

*Biofilms/growth & development
*Ecosystem
*Biodiversity
Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
Cyanobacteria/genetics/classification
Hydrology
Droughts
Floods
Metagenomics

@article {pmid41956535,
year = {2026},
author = {Cui, T and Huang, M},
title = {Tuberculous Peritonitis Diagnosed by Metagenomic Next-Generation Sequencing Progressing to Fatal Encapsulating Peritoneal Sclerosis in a Peritoneal Dialysis Patient: A Case Report.},
journal = {Seminars in dialysis},
volume = {},
number = {},
pages = {},
doi = {10.1111/sdi.70022},
pmid = {41956535},
issn = {1525-139X},
support = {SZSM202411016//Sanming Project of Medicine in Shenzhen/ ; },
abstract = {A 40-year-old woman on peritoneal dialysis for 3 years presented with febrile peritonitis. Metagenomic next-generation sequencing (mNGS) confirmed Mycobacterium tuberculosis complex in ascitic fluid, leading to prompt anti-tuberculosis therapy. She initially improved but developed ultrafiltration failure 15 months later and transitioned to hemodialysis. At 18 months, she developed bowel obstruction, bloody ascites, and characteristic imaging and laparoscopic findings of encapsulating peritoneal sclerosis (EPS). Despite supportive care, she deteriorated and died 30 months after tuberculosis peritonitis diagnosis. This case highlights that mNGS enables rapid diagnosis of tuberculous peritonitis when conventional tests are inconclusive, and that tuberculosis peritonitis may serve as a potent inflammatory trigger for EPS even after peritoneal dialysis cessation. Early recognition and timely intervention may improve outcomes.},
}

@article {pmid41956809,
year = {2026},
author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J},
title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336025},
pmid = {41956809},
issn = {1468-3288},
abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.

OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.

DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.

RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.

CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.},
}

@article {pmid41957175,
year = {2026},
author = {Yang, S and Wang, X and Duan, J and Yang, S and He, J and Fang, C and Zhao, N and Huang, Y},
title = {Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47725-x},
pmid = {41957175},
issn = {2045-2322},
support = {2022YFD1901500, 2022YFD1901505//National Key R&D Program Project/ ; ZSYS[2025]035//Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform)/ ; grant number BQW[2024]009//Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province/ ; },
abstract = {Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving "carbon-compensation" mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO3[-]-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a "stoichiometry-community diversity" cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.},
}

@article {pmid41957291,
year = {2026},
author = {Yang, M and Fang, J and Liao, Q},
title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41957291},
issn = {1434-9949},
}

@article {pmid41957365,
year = {2026},
author = {Kan, J and Spotton, K and Morales-Amador, A and Hernandez, Y and Burian, J and Panfil, C and Ternei, MA and Boer, RE and Bhattacharjee, A and Brady, SF},
title = {Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71586-7},
pmid = {41957365},
issn = {2041-1723},
support = {R35GM122559//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NIH T32 GM136640//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The discovery of natural products with specific modes of action from metagenomes remains challenging. Here, we present resistance-CONKAT-seq, a pipeline that links biosynthetic gene clusters (BGCs) to self-resistance genes, enabling identification of metabolites with desired molecular targets. Using clpP-directed resistance-CONKAT-seq, we identify the calprotamides, which activate native ClpP and enhance its activity. Cryo-EM and bioinformatic analyses reveal that the calprotamides' medium-chain N-acylphenylalanine substructure is a convergently evolved ClpP-targeting motif and identify additional BGCs predicted to encode this moiety, including some with co-localized clp genes. The synthesis of structures bioinformatically inspired by two such clp-linked BGCs, desmethyl jomthonic acid C and tuscamide, reveals that both enhance ClpP activity. Extending our bioinformatically guided synthesis study to additional BGCs lacking nearby clp genes shows that ClpP activity enhancement correlated with antibacterial activity, with the strongest enhancers exhibiting narrow-spectrum antibiotic activity. These findings establish N-acylphenylalanine as a previously unrecognized but common natural motif for targeting ClpP, which should help guide the discovery of both natural and synthetic ClpP modulators for antibiotic and anticancer development. Resistance-CONKAT-seq offers a scalable method for exploring biosynthetic dark matter for metabolites with desired modes of action.},
}

@article {pmid41947210,
year = {2026},
author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J},
title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02403-y},
pmid = {41947210},
issn = {2049-2618},
support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.

RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.

CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.},
}

@article {pmid41947478,
year = {2026},
author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G},
title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70205},
pmid = {41947478},
issn = {1099-1573},
support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; },
abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.},
}

@article {pmid41947790,
year = {2026},
author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X},
title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1744020},
pmid = {41947790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation & purification ; Metagenome ; Chronic Disease ; Aged ; },
abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.

METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.

RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable α-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.

CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome
*Mycobiome
*Constipation/microbiology/virology
Metagenomics
Feces/microbiology/virology
Female
*Bacteria/classification/genetics/isolation & purification
Male
Middle Aged
*Fungi/classification/genetics/isolation & purification
Adult
Dysbiosis/microbiology
Viruses/classification/genetics/isolation & purification
Metagenome
Chronic Disease
Aged

@article {pmid41948038,
year = {2026},
author = {Howells, AEG and Santana, M and Cook, EM and Orrill, B and Boyer, G and Debes, RV and Fecteau, KM and Colman, DR and Boyd, ES and Shock, EL},
title = {Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1736896},
pmid = {41948038},
issn = {1664-302X},
abstract = {Methane oxidation in terrestrial geothermal systems is an understudied process contributing to carbon cycling in extreme environments. We combined geochemical analyses, 16S rRNA gene amplicon sequencing, shotgun metagenome sequencing, and [14]CH4 microcosm assays across 61 Yellowstone hot springs spanning pH 1.9-9.0 and temperatures of 28.6-92.2 °C to survey hydrothermal systems for methanotrophy. Bacterial aerobic methanotroph phylotypes were detected at multiple sites, including Verrucomicrobia (order S-BQ2-57) and Alphaproteobacteria, with the family Methylocystaceae having the highest relative abundance among bacterial methanotroph phylotypes. No known archaeal anaerobic methanotrophs were observed. Biological methane oxidation was widespread, occurring at 14 of 17 experimental sites under both ambient and air-amended conditions. Rates were highest at CH4-rich, NH3-poor sites dominated by bacterial methanotrophs, consistent with energy supply predictions integrating CH4/O2 and CH4/NH3 concentration ratios. Conversely, NH3-rich, energy-rich sites exhibited lower methane oxidation rates (MOR) and were dominated by archaeal ammonia oxidizers, primarily Candidatus Nitrosocaldus, suggesting chemical competitive inhibition of NH3 on methanotrophy. Remarkably, significant methane oxidation occurred at eight sites where no known methanotrophs were detected, including a site at 89.9 °C-well above the previously reported upper growth temperature limit for methanotrophs from continental geothermal and hydrothermal systems-pointing to uncharacterized thermophilic lineages. These results suggest that biological methane oxidation in Yellowstone hot springs is influenced by the interplay of substrate availability and energy supply. By linking energy supply calculations with microbial distributions, we identify both known methanotrophs (Verrucomicrobia, Alphaproteobacteria) and archaeal ammonia oxidizers as potential active contributors, while highlighting the potential for novel thermophilic lineages, thereby expanding the ecological and thermal boundaries of methane oxidation in extreme terrestrial ecosystems.},
}

@article {pmid41948759,
year = {2026},
author = {Zhu, G and Zou, Z and Fang, Z and Xu, B},
title = {Rare but Critical: Severe Tropheryma Whipplei Pneumonia-Induced Cardiopulmonary Failure in a Young Immunocompromised Adult-A Case Report and Literature Review.},
journal = {Clinical case reports},
volume = {14},
number = {4},
pages = {e72448},
pmid = {41948759},
issn = {2050-0904},
abstract = {Tropheryma whipplei, traditionally linked to classic Whipple's disease with gastrointestinal involvement, is increasingly recognized as a cause of pneumonia. Reports of T. whipplei-associated pneumonia progressing to respiratory failure with concurrent acute cardiac failure remain extremely rare. A 38-year-old man with poorly controlled diabetes presented to the emergency department with acute chest tightness, dyspnea, and impaired consciousness. Laboratory findings indicated type II respiratory failure and elevated inflammatory markers. Imaging revealed scattered patchy hazy opacities and increased density bilaterally, prompting emergent intubation and transfer to the intensive care unit. Despite empirical antibiotics for severe pneumonia, he developed acute cardiac failure on day 3, manifesting as bloody sputum and diffuse moist rales with rhonchi on auscultation, alongside an LVEF of 49% and a markedly elevated serum BNP level of 3100 pg/mL. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected abundant T. whipplei sequences. He was administered targeted therapy with meropenem, supported by mechanical ventilation, diuresis, and glycemic control. Cardiopulmonary function improved, and he was discharged on oral doxycycline plus hydroxychloroquine. Follow-up endoscopy and biopsy showed no gastrointestinal involvement (Periodic Acid-Schiff negative), restored cardiac function (LVEF 58.6%), and no recurrence. This case underscores T. whipplei as a potential cause of isolated pneumonia with cardiopulmonary failure in functionally immunocompromised hosts and highlights the critical role of mNGS in guiding timely targeted therapy to improve outcomes.},
}

@article {pmid41949195,
year = {2026},
author = {Saini, G and Yadav, R and Bagga, R and Sharma, N and Sethi, S},
title = {Cervicovaginal microbiota in female sex workers with bacterial vaginosis: A metagenomic perspective.},
journal = {Indian journal of dermatology, venereology and leprology},
volume = {},
number = {},
pages = {1-3},
doi = {10.25259/IJDVL_1199_2025},
pmid = {41949195},
issn = {0973-3922},
}

@article {pmid41949263,
year = {2026},
author = {Marriott, L and Martinez-Lopez, A and Liga, A and Horiba, K and Warr, A and Phulusa, JN and Kumar, RS and Carey, L and Ito, Y and Parcell, BJ and Leslie, NR and Feasey, NA and Jacob, ST and Rylance, J and Kersaudy-Kerhoas, M},
title = {An automated and portable platform for rapid cell-free DNA isolation and its application in microbial DNA metagenomic sequencing from human blood samples.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5lc00876j},
pmid = {41949263},
issn = {1473-0189},
abstract = {The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days and is positive in less than 15% of cases, with many prevalent pathogens difficult or impossible to culture. While microbial cfDNA in blood could facilitate the diagnosis of sepsis, febrile and infectious conditions, sample preparation for cell-free DNA (cfDNA) analysis in decentralised settings presents challenges due to its complexity and the low concentration and fragmented nature of cfDNA in blood plasma. We developed a portable and automated platform and a consumable (CNASafe) for cfDNA isolation from human plasma samples. The platform-device performance was evaluated by comparing relative cfDNA yield against a reference (QIAGEN QIAamp Circulating Nucleic Acid Kit). cfDNA eluates from ten non-cultured blood samples from hospital patients were sequenced on a nanopore sequencer, and results compared to blood cultures. Extraction of cfDNA using the CNASafe device was completed in 40 minutes, compared to the 1 hour 15 min reference protocol. The device achieved an average relative cfDNA recovery of 100.5% over 333 unique extractions encompassing all parameter variations, demonstrating a performance equivalent to the reference kit. From the patient samples, a sufficient quantity of microbial cfDNA was extracted to either identify pathogens missed by blood cultures or confirm negative cultures. The CNASafe platform and real-time nanopore sequencing offer a promising solution for the rapid deployment of metagenomic diagnostics, enabling pathogen identification within a few hours in decentralised clinical environments.},
}

@article {pmid41949675,
year = {2026},
author = {Chen, Y and Sun, N and Gan, B and He, Y and Luo, J and Pan, K and Zeng, Y and Jing, B and Zeng, D and Ni, X},
title = {Targeting Bifidobacterium animalis alleviates high-fluoride exposure-induced kidney injury in mice.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02031-7},
pmid = {41949675},
issn = {2191-0855},
support = {2025YFHZ0278//Sichuan Science and Technology Program/ ; },
}

@article {pmid41949810,
year = {2026},
author = {Adolph, JE and Pentek, C and Bauch, T and Held, C and Brenner, T and Felderhoff-Müser, U and Grumaz, S and Horvatek, P and Steindor, M and Asar, L and Voigt, S and Dziobaka, J and Dohna-Schwake, C and Goretzki, SC},
title = {Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.},
journal = {Molecular and cellular pediatrics},
volume = {13},
number = {1},
pages = {},
pmid = {41949810},
issn = {2194-7791},
abstract = {BACKGROUND: Rapid and accurate pathogen detection is critical for optimizing outcomes in pediatric sepsis. Next-generation sequencing (NGS) of cell-free DNA (cfDNA) from blood enables culture-independent identification of microbial DNA from bacteria, viruses, fungi, and parasites. We evaluated the diagnostic yield and clinical impact of cfDNA-based NGS in critically ill and predominantly immunocompromised pediatric patients (≤ 18 years) with suspected infection. This retrospective single-center study included pediatric patients who underwent plasma cfDNA-NGS at a tertiary care hospital in Germany. Following computational removal of human DNA, remaining sequences were aligned to curated microbial reference databases. Diagnostic performance was compared with blood cultures and viral PCR, and clinical relevance was assessed by pediatric infectious disease specialists.

RESULTS: 111 tests in 78 pediatric patients, mostly with systemic inflammatory response syndrome of unknown etiology, were performed. Overall, 61 tests (54.5%) were positive for pathogenic cfDNA. Compared with conventional microbiological diagnostics, NGS demonstrated a sensitivity of 64.7% and specificity of 88.2% when blood cultures and viral PCR served as the reference standard. NGS identified additional pathogens in a substantial proportion (41.1%) of cases that remained negative by standard testing. Of those pathogens only found by NGS, over 60% were deemed clinically relevant. In 14.8% of positive NGS results, a pathogen-specific therapy was started, while 40.2% of tests led to a discontinuation of therapy (51.0% of negative tests). Out of all positive NGS, 38 (62.3%) were classified as clinically relevant. NGS testing also detected rare infections with fungi and parasites in four cases each.

CONCLUSION: Detection of pathogenic cfDNA through NGS from blood shows promising results as an additional diagnostic tool in critically ill pediatric patients with suspected infections. Clinical utility is currently still limited by its high cost, undetermined diagnostic validity and limitations in testing for resistances and restricted availability of raw sequencing data due to data-protection constraints.},
}

@article {pmid41949970,
year = {2025},
author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A},
title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.},
journal = {La Tunisie medicale},
volume = {103},
number = {11},
pages = {1707-1717},
doi = {10.62438/tunismed.v103i11.6101},
pmid = {41949970},
issn = {2724-7031},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/therapy ; *Dysbiosis/therapy/microbiology/etiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Hypoglycemic Agents/therapeutic use ; Insulin Resistance ; },
abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.},
}

Humans
*Diabetes Mellitus, Type 2/complications/microbiology/therapy
*Dysbiosis/therapy/microbiology/etiology
*Gastrointestinal Microbiome/drug effects/physiology
Probiotics/therapeutic use
Hypoglycemic Agents/therapeutic use
Insulin Resistance

@article {pmid41950191,
year = {2026},
author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT},
title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0344367},
doi = {10.1371/journal.pone.0344367},
pmid = {41950191},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Aquaculture ; *Drug Resistance, Microbial/genetics ; *Fishes/microbiology ; Genomics ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Microbial Sensitivity Tests ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.},
}

Animals
Bangladesh
*Chickens/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
Aquaculture
*Drug Resistance, Microbial/genetics
*Fishes/microbiology
Genomics
Anti-Bacterial Agents/pharmacology
Biodiversity
Microbial Sensitivity Tests
Metagenomics
*Drug Resistance, Bacterial/genetics

@article {pmid41950533,
year = {2026},
author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X},
title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128511},
doi = {10.1016/j.micres.2026.128511},
pmid = {41950533},
issn = {1618-0623},
abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.},
}

@article {pmid41950684,
year = {2026},
author = {Cao, S and Liu, X and Tao, Y and Ren, J and Zhou, Z and Du, R},
title = {EPS-mediated mineralization drives granule densification and enhances denitratation-anammox coupling under alkaline conditions.},
journal = {Water research},
volume = {299},
number = {},
pages = {125888},
doi = {10.1016/j.watres.2026.125888},
pmid = {41950684},
issn = {1879-2448},
abstract = {The granular-based CANDAN (Complete Ammonium and Nitrate removal via Denitratation-Anammox over Nitrite) process offers a promising low-carbon and high-rate strategy for nitrogen removal; yet the mechanisms by which alkaline conditions regulate granule structure and functional coupling remain insufficiently understood. Here, a 9-L sequencing batch reactor (SBR) was operated for 130 days with stepwise pH elevation from 7.31 ± 0.03 to 8.52 ± 0.08 to elucidate alkaline condition-driven structural and functional adaptations in CANDAN granules. Moderate alkaline conditions significantly improved nitrogen removal, with total nitrogen removal efficiency increasing to 91.4 ± 0.1 %, accompanied by pronounced improvement in sludge settleability (sludge volume index after 30 min of settling, SVI30, decreased from 76.4 to 19.4 mL g[-1] SS) and stabilization of dominant granule sizes at 0.5-1 mm, accounting for approximately 69.8 % of the total granules, indicating progressive granule densification. Mineralogical analyses revealed that hydroxyapatite dominated the inorganic matrix, with co-precipitation of calcium carbonate (CaCO3) and transient magnesium ammonium phosphate formation reinforcing granule structure. Elevated pH also remodeled extracellular polymeric substances (EPS), increasing loosely bound EPS, raising the protein-to-polysaccharide ratio, and enriching tryptophan-like proteins that facilitated EPS-mediated mineral nucleation. Metagenomic analysis revealed streamlined carbon metabolism and enrichment of key nitrogen-cycling genes (napA, nosZ, hzsA), while downregulation of Ca[2+], Mg[2+], and phosphate transport genes favored extracellular mineral accumulation. Overall, moderately alkaline conditions drive EPS-mediated mineralization that densifies granules and stabilizes Denitratation-Anammox coupling, providing mechanistic insight for optimizing low-carbon nitrogen removal under alkaline wastewater conditions.},
}

@article {pmid41950685,
year = {2026},
author = {Zuo, Z and Xing, Y and Qiao, L and Yang, S and Ren, D and Guo, M and Liu, Y and Huang, X},
title = {Unveiling in-pipe carbon-sulfur transformation and microbial function during urine transport for centralized management.},
journal = {Water research},
volume = {299},
number = {},
pages = {125840},
doi = {10.1016/j.watres.2026.125840},
pmid = {41950685},
issn = {1879-2448},
abstract = {Source-separated urine collection and centralized nutrient recovery at city-scale hold great potential for advancing sustainable resource management. As the critical link between urine collection systems and nutrient recovery facilities, urine-transporting sewer systems have recently been incorporated into life cycle assessments (LCA), yet their potential for biochemical transformations has not been explored. Here, for the first time, we experimentally unveil key pollutant transformations and microbial functions in a urine-fed bioreactor (representing urine transport), with a sewage-fed bioreactor serving as a control. Major urine nutrients (N, P, and K) remained largely stable during transport, whereas organic carbon and sulfate decreased markedly. Methane production was negligible over 160 days, while sulfide production initially declined but fully recovered by day 80, accompanied by elevated microbial activity and substantial sulfide accumulation in sediments. Microbial community analyses revealed that urine exposure reduced community richness and led to a pronounced community, with methanogenic archaea strongly inhibited and sulfate-reducing bacteria (SRB) becoming dominant under prolonged urine stress. A Desulfomicrobium-like SRB species was progressively enriched (∼35% of total metagenome-assembled genomes (MAGs)) and likely responsible for the sulfide rebound. Spatial heterogeneity of microbial communities in sediments further explains depth-specific sulfide accumulation. Overall, this study provides important insights into carbon-sulfur transformations and microbial adaptation in urine transport systems, informing improved system design, operation, and further LCA.},
}

@article {pmid41950966,
year = {2026},
author = {Yan, S and Han, Q and Chen, L and Jin, D and Lu, Y and Zhou, J and Zhang, X},
title = {Simultaneous removal of Se(IV) and Cr(VI) from acidic wastewater using a Se(IV)-reducing internal circulation reactor: performance and microbial resistance mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134537},
doi = {10.1016/j.biortech.2026.134537},
pmid = {41950966},
issn = {1873-2976},
abstract = {Acidic wastewater contaminated with selenite (Se(IV)) and chromate (Cr(VI)) poses elevated environmental risks due to the combined toxicity of metal(liod) and acidity. Metal(loid)-resistant consortia, such as Se(IV)-reducing sludge (SeRS), provide a promising strategy for treating such wastewater by converting Se(IV) and Cr(VI) into less toxic Se(0) and Cr(III), respectively. In this study, an internal circulation (IC) reactor loaded with SeRS and granular activated carbon was constructed to evaluate its performance in treating such wastewater. In the absence of Cr(VI), the reactor achieved 94.6-98.5% Se(IV) removal at influent pH 4.5-8.0 with 1-3 mM Se(IV). At optimal pH 5.5, nearly complete removal of both oxyanions was achieved at Se(IV)/Cr(VI) molar ratio of 5.2-10.4. Alkalinity generation from acetate oxidation buffered influent acidity at influent pH 4.5-5.5 and sustained microbial activity. Cr(VI) stress selectively enriched Brucella, Trichlorobacter, and Seleniivibrio for Cr(VI) reduction, while Pseudomonas accounted for Se(IV) and Cr(VI) reduction. Integrated extracellular polymeric substances (EPS), glutathione reductase (GOR), and metagenomic analyses revealed microbial resistance to Cr(VI) stress likely relied on intracellular glutathione-related detoxification, enzymatic Se(IV)/Cr(VI) reduction and antioxidant defenses, while extracellular EPS protection declined. Overall, it was demonstrated that the developed IC reactor process enabled robust and efficient removal of both Se(IV) and Cr(VI) from acidic wastewater.},
}

@article {pmid41951175,
year = {2026},
author = {Rana, N and Angrup, A and Tiewsoh, K and Ray, P},
title = {Automating Microbial Community Analysis (AMCA): Development and application of as amplicon based graphical pipeline in patients with Chronic Kidney Disease.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101110},
doi = {10.1016/j.ijmmb.2026.101110},
pmid = {41951175},
issn = {1998-3646},
abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.

METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.

RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.

CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.},
}

@article {pmid41951362,
year = {2026},
author = {Kariya, E and Tirard-Collet, P and Boulagnon-Rombi, C and Destras, G and Wallon, M and Menotti, J and Lapendry, A and Kaidi, N and Rabodonirina, M and Lievre, L and Depaquit, J and Villena, I and Trecourt, A and Huguenin, A},
title = {Integrated histomolecular diagnosis of mesenteric anisakiasis.},
journal = {Journal of clinical pathology},
volume = {},
number = {},
pages = {},
doi = {10.1136/jcp-2026-210635},
pmid = {41951362},
issn = {1472-4146},
abstract = {A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.},
}

@article {pmid41951635,
year = {2026},
author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S},
title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07154-x},
pmid = {41951635},
issn = {2052-4463},
abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.},
}

@article {pmid41951715,
year = {2026},
author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL},
title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09820-7},
pmid = {41951715},
issn = {2399-3642},
abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.},
}

@article {pmid41951791,
year = {2026},
author = {Somerville, TF and Kaye, SB},
title = {Comment on: 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections'.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {41951791},
issn = {1476-5454},
}

@article {pmid41951875,
year = {2026},
author = {Wang, Y and Li, Y and Fang, J and Huang, Z and Zhang, C and Xu, B},
title = {A Novel Broad pH-Adaptive Bile Salt Hydrolase from Nomascus concolor Fecal Microbial Metagenome Facilitates the Cholesterol-Lowering Ability of Escherichia coli Nissle 1917.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41951875},
issn = {1867-1314},
support = {32360034//National Natural Science Foundation of China/ ; },
}

@article {pmid41943240,
year = {2026},
author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J},
title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {4},
pages = {e70421},
doi = {10.1002/iid3.70421},
pmid = {41943240},
issn = {2050-4527},
support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; },
mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid/immunology ; *SARS-CoV-2 ; *Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology ; *Area Postrema/virology/pathology ; Middle Aged ; Adult ; Magnetic Resonance Imaging ; Immunoglobulin G/blood/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/blood ; },
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.

METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.

RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.

CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.},
}

Humans
Female
*COVID-19/complications/cerebrospinal fluid/immunology
*SARS-CoV-2
*Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology
*Area Postrema/virology/pathology
Middle Aged
Adult
Magnetic Resonance Imaging
Immunoglobulin G/blood/cerebrospinal fluid
Aquaporin 4/immunology
Autoantibodies/blood

@article {pmid41943413,
year = {2026},
author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J},
title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {75-83},
doi = {10.33073/pjm-2026-008},
pmid = {41943413},
issn = {2544-4646},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; Aged ; Bacteria/genetics/isolation & purification/classification ; *Pneumonia/microbiology/blood/complications/diagnosis ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Adult ; *Sepsis/microbiology/diagnosis ; },
abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology/virology
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Retrospective Studies
Middle Aged
*Metagenomics/methods
Aged
Bacteria/genetics/isolation & purification/classification
*Pneumonia/microbiology/blood/complications/diagnosis
Fungi/genetics/isolation & purification/classification
Aged, 80 and over
Adult
*Sepsis/microbiology/diagnosis

@article {pmid41943678,
year = {2026},
author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J},
title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70843},
doi = {10.1111/gcb.70843},
pmid = {41943678},
issn = {1365-2486},
support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Biodiversity ; China ; *Soil/chemistry ; *Fungi/physiology ; Ecosystem ; *Sodium/analysis ; Salinity ; },
abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.},
}

*Soil Microbiology
*Biodiversity
China
*Soil/chemistry
*Fungi/physiology
Ecosystem
*Sodium/analysis
Salinity

@article {pmid41944124,
year = {2026},
author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W},
title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10074},
pmid = {41944124},
issn = {1520-5851},
abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.},
}

@article {pmid41944276,
year = {2026},
author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R},
title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13821},
pmid = {41944276},
issn = {1520-5851},
abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.},
}

@article {pmid41944309,
year = {2026},
author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L},
title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17245},
doi = {10.1002/advs.202517245},
pmid = {41944309},
issn = {2198-3844},
support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.},
}

@article {pmid41946009,
year = {2026},
author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P},
title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.},
journal = {Enzyme and microbial technology},
volume = {198},
number = {},
pages = {110869},
doi = {10.1016/j.enzmictec.2026.110869},
pmid = {41946009},
issn = {1879-0909},
abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.},
}

@article {pmid41946242,
year = {2026},
author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L},
title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141986},
doi = {10.1016/j.jhazmat.2026.141986},
pmid = {41946242},
issn = {1873-3336},
abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.},
}

@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}

@article {pmid41946403,
year = {2026},
author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y},
title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134561},
doi = {10.1016/j.biortech.2026.134561},
pmid = {41946403},
issn = {1873-2976},
abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.},
}

@article {pmid41946559,
year = {2026},
author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S},
title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.},
journal = {The British journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1136/bjo-2025-328867},
pmid = {41946559},
issn = {1468-2079},
abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.

METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.

RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; κ=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; κ=0.78), though accuracy remained below specialists (87-90%; κ≈0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; κ=0.95; GPT-5 91.7%; κ=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.

CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.},
}

@article {pmid41889817,
year = {2026},
author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL},
title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41889817},
issn = {2692-8205},
abstract = {Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.},
}

@article {pmid41937465,
year = {2026},
author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT},
title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2508050},
doi = {10.4014/jmb.2508.08050},
pmid = {41937465},
issn = {1738-8872},
mesh = {*Petroleum/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Salinity ; Soil Microbiology ; Metagenomics/methods ; Biodegradation, Environmental ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.},
}

*Petroleum/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
*Salinity
Soil Microbiology
Metagenomics/methods
Biodegradation, Environmental
Soil Pollutants/metabolism
Hydrocarbons/metabolism
*Microbiota
Phylogeny

@article {pmid41937665,
year = {2026},
author = {Sizikova, TE and Lebedev, VN and Borisevich, SV},
title = {The Mengla virus (Filoviridae: Dianlovirus).},
journal = {Voprosy virusologii},
volume = {71},
number = {1},
pages = {7-12},
doi = {10.36233/0507-4088-356},
pmid = {41937665},
issn = {2411-2097},
mesh = {Animals ; *Chiroptera/virology/genetics ; *Filoviridae/genetics/classification/pathogenicity/isolation & purification ; Humans ; Phylogeny ; Genetic Variation ; Genome, Viral ; *Filoviridae Infections/virology/epidemiology/genetics ; Asia, Southeastern/epidemiology ; Hemorrhagic Fever, Ebola/virology/genetics/epidemiology ; },
abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.

MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.

RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.

CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.},
}

Animals
*Chiroptera/virology/genetics
*Filoviridae/genetics/classification/pathogenicity/isolation & purification
Humans
Phylogeny
Genetic Variation
Genome, Viral
*Filoviridae Infections/virology/epidemiology/genetics
Asia, Southeastern/epidemiology
Hemorrhagic Fever, Ebola/virology/genetics/epidemiology