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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42863958,
year = {2026},
author = {Qin, H and Wang, W and Chen, E and Sheng, R and Zhu, B},
title = {Long-Term Fertilisation Shapes the Distribution and N2O Reduction Potential of Clade I and Clade II N2O Reducers Along the Soil Profile in Rice Paddies.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70452},
doi = {10.1111/1462-2920.70452},
pmid = {42863958},
issn = {1462-2920},
support = {U24A20356//National Natural Science Foundation of China/ ; 2025YFE0122400//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Nitrous Oxide/metabolism ; *Fertilizers/analysis ; *Oryza/growth & development ; *Soil/chemistry ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Nitrogen/metabolism ; Oxidation-Reduction ; Metagenome ; },
abstract = {Long-term fertilisation alters nitrous oxide (N2O) emissions from paddy soils, but its effects on the ecological roles of distinct N2O-reducing clades remain unclear. Here, we investigated Clade I and Clade II N2O reducers using a 20-year field experiment with unfertilized control (CK), chemical fertilizer (NPK), and organic fertilizer (OF) treatments. Clade II dominated the community, accounting for 72.4% of nosZ reads and 83.3% of recovered nosZ-containing draft metagenome-assembled genomes (MAGs), and was enriched in carbohydrate-active enzyme (CAZy) genes. However, Clade I abundance explained more variation in soil N2O reduction potential than Clade II (R[2] = 0.38 vs. 0.28). Structural equation modelling showed that fertilisation enhanced soil carbon and nitrogen status, which strongly promoted Clade I abundance (β = 0.90). Clade I fully mediated fertilisation effects on N2O reduction potential, whereas Clade II showed only partial mediation. The two clades also exhibited contrasting vertical distributions: Clade I was relatively uniform throughout the soil profile, while Clade II displayed niche stratification, with different taxa dominating surface, middle, and deep layers. These results suggest distinct ecological strategies of the two N2O-reducing clades and long-term fertilisation differentially influences their distribution and contribution to the N2O sink function of rice paddy soils during the period examined.},
}

*Soil Microbiology
*Nitrous Oxide/metabolism
*Fertilizers/analysis
*Oryza/growth & development
*Soil/chemistry
*Bacteria/metabolism/classification/genetics/isolation & purification
Nitrogen/metabolism
Oxidation-Reduction
Metagenome

@article {pmid42864071,
year = {2026},
author = {Li, S and Kong, Y and Liu, Y and Chen, Y and Ji, M and Yang, Y and Chen, Y},
title = {Metabolic Versatility Drives the Late-Successional Dominance of Ammonia-Oxidizing Archaea in Retreating Glacier Soils.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70450},
doi = {10.1111/1462-2920.70450},
pmid = {42864071},
issn = {1462-2920},
support = {25RCKA021//Science and Technology Department of Gansu Province/ ; 42425607//National Natural Science Foundation of China/ ; lzuibky-2024-oy01//Lanzhou University/ ; },
mesh = {*Ammonia/metabolism ; *Soil Microbiology ; *Archaea/metabolism/genetics/classification ; Oxidation-Reduction ; Nitrification ; *Ice Cover/microbiology ; Bacteria/metabolism/genetics/classification ; Tibet ; Soil/chemistry ; Nitrogen/metabolism ; },
abstract = {Climate warming accelerates glacier retreat, creating glacier forefields that serve as critical chronosequences for studying nitrogen cycling succession. Ammonia-oxidizing microorganisms (AOMs) play key roles in regulating nitrogen availability for organic carbon accumulation and plant colonization. However, the underlying metabolic mechanisms governing these successional shifts and their functional consequences for nitrification potential remain poorly understood. Here, we integrated soil physicochemical and nitrification potential measurements with a multi-omics approach (qPCR, amplicon and metagenomic sequencing) across four successional stages at the Kuoqionggangri Glacier forefield, Tibetan Plateau. Results revealed a shift from ammonia-oxidizing bacteria (AOB, primarily Nitrosospira) dominance in barren ground to ammonia-oxidizing archaea (AOA, Nitrososphaerales) dominance in meadows, driven by environmental filtering (lowered pH, increased moisture, carbon, nitrogen). Additionally, metagenomic binning showed that AOA possessed broad metabolic capacities for cycling carbon, nitrogen, sulphur and phosphorus. This metabolic versatility conferred a superior adaptive advantage, driving AOA dominance and a corresponding increase in nitrification potential. Furthermore, elevated nitrification potential was jointly driven by shifts in the AOM community and environmental variables. These findings suggest that environmental filtering and AOA metabolic versatility contribute to AOA success in late-successional soils, establishing a dual-mechanism framework for nitrification dynamics during proglacial ecosystem succession.},
}

*Ammonia/metabolism
*Soil Microbiology
*Archaea/metabolism/genetics/classification
Oxidation-Reduction
Nitrification
*Ice Cover/microbiology
Bacteria/metabolism/genetics/classification
Tibet
Soil/chemistry
Nitrogen/metabolism

@article {pmid42864526,
year = {2026},
author = {Chang-Sheng, L and Feng-Jun, L and Huan-Sheng, L and Qiang, H and Zong-Ke, Z},
title = {The boundary between microbial detection and implant-related infection: a structured narrative review of analytical credibility, biological persistence, host response, and clinical causality.},
journal = {Archives of orthopaedic and trauma surgery},
volume = {146},
number = {1},
pages = {},
pmid = {42864526},
issn = {1434-3916},
mesh = {Humans ; *Prosthesis-Related Infections/microbiology/diagnosis ; Biofilms ; Hardware Removal ; Device Removal ; },
abstract = {BACKGROUND: Unexpected microbial signals are frequently encountered in patients with orthopaedic implants who do not satisfy validated criteria for confirmed infection. The central interpretive problem is not limited to periprosthetic joint infection (PJI); it also arises in fracture-fixation and spinal instrumentation, and it involves conventional culture, sonication, histopathology, broad-range polymerase chain reaction (PCR), 16 S rRNA sequencing, and metagenomic next-generation sequencing (mNGS).

METHODS: We performed a structured narrative review of literature identified in PubMed, Embase, and Web of Science, updated through 27 June 2026. Eligible publications addressed microbial or biofilm-associated signals in orthopaedic implants without unequivocal infection at the time of sampling, or reported outcomes after unexpected positive cultures. Evidence was organized by implant type, indication for implant removal, detection method, host-response evidence, and longitudinal outcome. Particular attention was paid to the distinction between routinely removed fracture-fixation devices and failure-related arthroplasty or spinal revisions.

RESULTS: Routine removal of fracture-fixation devices provides the least confounded clinical window and demonstrates that microbial signals may be recovered from implants in the absence of recognized failure or overt infection. By contrast, arthroplasty and spinal cohorts labelled "presumed aseptic" are intrinsically confounded because pain, loosening, osteolysis, or pseudarthrosis may represent occult infection. Molecular positivity is further limited by low-biomass contamination and inability to distinguish viable organisms from relic DNA. Favorable outcomes after revision do not prove that infection was never present, because revision surgery itself may eradicate or substantially reduce an occult microbial burden.

CONCLUSIONS: Microbial detection should be interpreted through three sequential domains: analytical credibility, biological activity or persistence, and clinical causality supported by host response or implant-related pathology. "Stable coexistence" is best treated as a longitudinal clinical phenotype or testable mechanistic hypothesis, not as an established diagnostic category. This framework complements, but does not replace, validated PJI, fracture-related infection (FRI), or other implant-specific definitions.},
}

Humans
*Prosthesis-Related Infections/microbiology/diagnosis
Biofilms
Hardware Removal
Device Removal

@article {pmid42864924,
year = {2026},
author = {Suresh, N and Singh, V and Rathore, A and Dwivedi, S and Bansal, A},
title = {The Gut Microbiota-inflammation-immune Axis in Cancer: Anti-inflammatory Mechanisms and Therapeutic Implications.},
journal = {Anti-inflammatory & anti-allergy agents in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715230502786261001104534},
pmid = {42864924},
issn = {1875-614X},
abstract = {Through its mediation between inflammatory and immune pathways, the gut microbiota has proved to be a key regulator of cancer development, progression, and treatment response. Changes in microbial composition known as dysbiosis might facilitate chronic inflammation, immune dysregulation, and genomic instability, thereby facilitating carcinogenesis. Conversely, positive commensal microbes can generate short-chain fatty acids, bile acids, and tryptophan derivatives, which help maintain the epithelial barrier, cytokine signaling, and innate and adaptive immune responses. These microbial metabolites regulate immune cell differentiation, including regulatory T cells, dendritic cells, macrophages, and cytotoxic CD8+ T cells, thereby impacting the tumor microenvironment and tumor progression. Recent research highlights the microbiota as an outcome of response to cancer therapies, particularly immune checkpoint inhibitors, chemotherapy, and targeted therapies. Certain microbial genera, e.g., Akkermansia muciniphila, Bifidobacterium species, and Faecalibacterium prausnitzii, have been linked to augmented antitumor immunity and treatment efficacy. To enhance treatment outcomes and minimize toxicity during therapy, therapeutic interventions that target the regulation of the gut microbiome, such as dietary interventions, probiotics, prebiotics, fecal microbiota transplantation, and engineered microbial platforms, are under investigation. Moreover, improvements in metagenomics, metabolomics, and immunomics are now enabling the discovery of microbiome-based biomarkers to inform precision oncology. Knowledge of the gut microbiota-inflammation-immune axis thus presents promising possibilities in creating new treatment modalities and in designing individualized treatments in cancer management.},
}

@article {pmid42865011,
year = {2026},
author = {Shur, G and Burstein, D},
title = {FAMUS: A Few-Shot Learning Framework for Large-Scale Protein Annotation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag761},
pmid = {42865011},
issn = {1367-4811},
abstract = {MOTIVATION: Gene function prediction is pivotal in genomic and metagenomic data analysis. Current annotation tools typically rely on the most similar sequence from the query database and struggle to robustly set meaningful hit thresholds, causing a major challenge for reliable annotation.

RESULTS: Here, we present a contrastive learning framework for functional annotation. FAMUS (Functional Annotation Method Using Supervised contrastive learning) compares query sequences to a full array of profile Hidden Markov Models, encoding each sequence's complete similarity profile, rather than only its top-scoring hit, into a condensed vector space that minimizes the distance between proteins from the same family. Unannotated sequences are incorporated as negative examples during training, enabling robust detection of proteins that fall outside the reference database without requiring user-defined thresholds. FAMUS outperformed KEGG's native KofamScan for KEGG Orthology annotation and InterPro's InterProScan for PANTHER family annotation, especially on realistic, sparsely annotated data. We used this approach to build four protein annotation models spanning the KEGG Orthology, InterPro, OrthoDB, and EggNOG databases. FAMUS is a comprehensive, modular framework that supports both pre-defined and user-specific databases. It can be readily integrated into genomic and metagenomic analysis pipelines for accurate, large-scale functional annotation.

All four models are available as a conda package and via our web server at https://app.famus.bursteinlab.org/, and source code is freely available on GitHub at https://github.com/burstein-lab/famus/ as well as a source code snapshot at https://doi.org/10.5281/zenodo.23132542.

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

@article {pmid42865259,
year = {2026},
author = {Doane, MP and Martin, B and Kerr, E and Dinsdale, EA and Rangers, MM and Guida, L and Kyne, PM},
title = {Patterns of Functional Redundancy and Anaerobic Metabolic Potential Characterise the Skin Microbiome of a Critically Endangered Sawfish.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70442},
doi = {10.1111/1462-2920.70442},
pmid = {42865259},
issn = {1462-2920},
support = {//Charles Darwin University 2021 Institute of Advanced Studies (IAS) Rainmaker Start Up/ ; //Australian Marine Conservation Society (AMCS)/ ; //Flinders Accelerator for Microbiome Exploration/ ; },
mesh = {Animals ; *Skin Microbiome ; Anaerobiosis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Endangered Species ; *Microbiota ; Metagenomics ; *Skin/microbiology ; Phylogeny ; },
abstract = {Using shotgun metagenomics of largetooth sawfish (Pristis pristis) skin and paired pool water samples, we provide the first taxonomic and functional characterisation of a sawfish skin microbiome and assess its ecological distinctiveness, assembly, and resilience relative to the surrounding water column. The skin microbiome was strongly host-associated and compositionally distinct, with lower taxonomic richness than the water column but dominated by Bacillota, particularly spore-forming Bacilli. Functional profiling revealed genes associated with sporulation, dormancy, anaerobic metabolism, and peptide transport, consistent with low-oxygen, low-flow conditions. In contrast, water-column microbiomes were more taxonomically diverse and enriched in phototrophic and polysaccharide-utilisation pathways. Sawfish skin communities exhibited patterns consistent with greater functional redundancy, with gene functions accumulating more rapidly per taxon. Together with greater among-individual taxonomic dispersion, this pattern is consistent with a host-filtered, lottery-like assembly process in which taxonomically variable communities maintain similar functional potential. The enrichment of dormancy and anaerobic pathways suggests the skin microbiome persists through periods of host quiescence and environmental stress while maintaining metabolic potential. Together, these results demonstrate that the sawfish skin supports a resilient, functionally robust microbiome distinct from ambient aquatic communities, highlighting the potential for integrating microbial functional data into conservation strategies for Critically Endangered vertebrates.},
}

Animals
*Skin Microbiome
Anaerobiosis
*Bacteria/classification/genetics/isolation & purification/metabolism
Endangered Species
*Microbiota
Metagenomics
*Skin/microbiology
Phylogeny

@article {pmid42865488,
year = {2026},
author = {Ye, Z and Liao, Y and Gao, Z and Chen, S and Huang, Q and Jin, P},
title = {Syphilitic bicuspid aortic valve endocarditis diagnosed by metagenomic next-generation sequencing: a case report and literature review.},
journal = {Frontiers in surgery},
volume = {13},
number = {},
pages = {1911873},
pmid = {42865488},
issn = {2296-875X},
abstract = {BACKGROUND: Syphilitic endocarditis, a rare complication of tertiary syphilis, poses diagnostic challenges due to the unculturable nature of Treponema pallidum and non-specific clinical manifestations. This report highlights the role of quantitative metagenomic next-generation sequencing (Q-mNGS) in confirming the diagnosis.

CASE PRESENTATION: A 52-year-old male patient with a bicuspid aortic valve presented with a cough and chest tightness. Serology confirmed syphilis, but blood cultures were negative. Transesophageal echocardiography revealed severe aortic regurgitation with vegetations. Q-mNGS of resected valve tissue detected T. pallidum despite negative Warthin-Starry staining. The patient underwent valve replacement and received penicillin G, with no recurrence at the 2-year follow-up.

CONCLUSIONS: Q-mNGS shows potentially higher sensitivity for diagnosing syphilitic endocarditis compared to traditional methods. Serological screening combined with molecular techniques is critical for culture-negative endocarditis in high-risk populations.},
}

@article {pmid42865524,
year = {2026},
author = {Yan, JY and Zhou, Y and Ni, L and Ding, ZJ and Lin, C},
title = {Effects of trait stacking on the maize phyllosphere microbiome: a shotgun metagenomic comparison.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1904641},
pmid = {42865524},
issn = {1664-302X},
abstract = {Current safety assessments for stacked-trait transgenic crops underrepresent the phyllosphere, a critical interface directly exposed to transgenic products, warranting strengthened risk evaluation. Here, we employed metagenomics to characterize the phyllosphere of three maize lines under herbicide-free conditions: wild-type (Corn.CK), herbicide-resistant single-trait (transgene of cp4-epsps, Corn.S), and insect- and herbicide-resistant stacked-trait (transgene of cry1Ab and cp4-epsps, Corn.D). Shannon diversity showed a consistent trend toward higher values in the cp4-epsps single-trait line than in the wild type (not significant after correction for multiple comparisons), whereas the stacked-trait line showed an intermediate increase. Transgenic events were associated with bidirectional taxonomic remodeling, characterized by the depletion of Enterobacterales and enrichment of environmentally adapted taxa. Functionally, transgenic lines displayed pervasive metabolic depletion across KEGG pathways and CAZyme categories, alongside reduced abundance of virulence-associated gene homologs (e.g., T6SS and Enterobactin) and lower antibiotic resistance gene diversity (wild-type > stacked-trait > single-trait), driven by the concomitant loss of Enterobacterales hosts. Notably, in most of the taxonomic, functional, virulence, and resistome dimensions examined, the stacked-trait line exhibited an intermediate microbiome profile between the wild-type and single-trait lines. These findings suggest that, for this genotype combination under these controlled conditions, trait stacking was not associated with microbiome perturbation greater than that observed for the single trait, and provide a preliminary, genotype- and stage-specific reference for phyllosphere biosafety assessment, pending field validation.},
}

@article {pmid42865541,
year = {2026},
author = {Yuan, D and Gu, C and Fang, Y and Yang, Q},
title = {Integrated pathogen detection and immune profiling in posner-schlossman syndrome: a metagenomic and cytokine approach.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1918795},
pmid = {42865541},
issn = {2296-634X},
abstract = {BACKGROUND: Posner-Schlossman syndrome (PSS) is recurrent unilateral anterior uveitis with severely elevated intraocular pressure disproportionate to visible inflammation. Cytomegalovirus (CMV) is linked to partial PSS cases, yet it is unknown whether CMV induces unique immune signatures or only amplifies baseline inflammation. We combined metagenomic next-generation sequencing (mNGS), multiplex cytokine detection and machine learning to clarify CMV's pathogenic role.

METHODS: This single-center prospective study recruited 52 untreated patients with acute PSS and 25 sex-matched cataract controls. Aqueous humor samples underwent mNGS pathogen testing to divide PSS patients into CMV-positive and CMV-negative groups, and cytometric bead array was used to quantify 9 immune mediators. Seven machine learning algorithms covering linear, kernel, ensemble tree, probabilistic and discriminant models were applied to distinguish CMV status, with XGBoost and LightGBM added to validate result stability. All models were built in Python 3.9.

RESULTS: mNGS identified CMV in 42.3% of PSS patients. Baseline clinical features were comparable between CMV subgroups. Six pro-inflammatory cytokines were significantly higher in PSS patients than controls, whereas no cytokine differed between CMV subgroups after Bonferroni correction. All seven models poorly discriminated CMV status; quadratic discriminant analysis yielded the maximum AUC of merely 0.552. SHAP values verified weak predictive power of cytokines, and learning curves indicated severe overfitting and limited generalizability within the evaluated range of training sample sizes.

CONCLUSION: Within the current sample size and measured cytokine panel, no statistically significant or stable difference in aqueous cytokine profiles was detected between CMV-positive and CMV-negative PSS patients, even with advanced machine learning methods. Our findings are consistent with the inflammation amplifier hypothesis, but the current cross-sectional data cannot definitively confirm CMV's biological role, nor rule out CMV as a primary pathogenic trigger in a subset of PSS cases. Direct pathogen detection is required for personalized antiviral treatment, and shared inflammatory pathways provide universal targets for novel immunomodulatory therapies for all PSS patients.},
}

@article {pmid42865799,
year = {2026},
author = {Luo, X and Li, Z and Ye, F},
title = {Clinical research advances in pulmonary infections in 2025: a narrative review of multipathogen assessment, precision diagnosis, and integrated management.},
journal = {Journal of thoracic disease},
volume = {18},
number = {9},
pages = {1062},
pmid = {42865799},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: The diagnosis and treatment of pulmonary infections have become increasingly complex owing to antimicrobial resistance, the growing population of immunocompromised patients, and the ongoing circulation of respiratory viruses. In this narrative review, the major clinical advances reported in 2025 are summarised, and evidence-based support for multipathogen assessment, precision diagnosis, individualized treatment, and integrated management of pulmonary infections is provided.

METHODS: PubMed, Web of Science, and the Chinese Medical Association Journal Database were searched for relevant English-language and Chinese-language publications. The search primarily focused on studies published in 2025 and was supplemented by the manual retrieval of relevant clinical studies and guidelines. Medical Subject Headings (MeSH) and free-text terms were used in PubMed, with corresponding free-text terms applied in the other databases. Clinically relevant publications were screened according to predefined criteria by two independent reviewers, and expert adjudication was used in the event of disagreements.

KEY CONTENT AND FINDINGS: Metagenomic next-generation sequencing (mNGS), integrated biomarker assessment, and artificial intelligence (AI) have exhibited increasing clinical value in pathogen identification, differential diagnosis, and prognostic assessment. Therapeutic advances have been reported for drug-resistant bacterial and fungal infections, as well as for coronavirus disease 2019 (COVID-19) and influenza, supporting more precise and individualized treatment. Studies on the gut-lung axis and immune modulation have further clarified the potential role of host-directed approaches, although clinical evidence for microbiota-targeted interventions remains limited. The risks associated with coinfection received increasing attention, while improved identification of risk factors and stratified management supported more individualized care for high-risk populations.

CONCLUSIONS: In 2025, the clinical management of pulmonary infections continued to transition towards precision-oriented and host-directed models. However, because a quantitative evidence synthesis was not included in this narrative review, pooled effect size estimates or formally graded clinical recommendations are not provided. The heterogeneity of the available studies also limits the overall strength and generalisability of the evidence. Future high-quality, multicentre studies are needed to further standardise clinical diagnosis and treatment strategies.},
}

@article {pmid42865986,
year = {2026},
author = {Chen, Y and Li, Y and Lu, H and Jia, S and Jiang, Y},
title = {New insights into the gut-heart axis: microbial metabolite biomarkers, multi-omics, and engineered bacterial delivery systems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1987882},
pmid = {42865986},
issn = {1664-302X},
abstract = {Despite rapid growth in gut-heart axis research, clinical translation remains limited. This review addresses that gap by critically synthesizing recent evidence on microbiota-derived metabolites, biomarkers, multi-omics workflows, and engineered bacterial interventions in cardiovascular disease (CVD). We examine how TMAO, short-chain fatty acids, bile acids, indole derivatives, and phenylacetylglutamine exert context-dependent cardiovascular effects, and why functional microbial gene markers and integrated biomarker panels may outperform single-taxon signatures. We then evaluate multi-omics strategies, metagenomics, metabolomics, proteomics, single-cell and spatial omics, and bioinformatics integration, for causal inference and biomarker validation. Finally, we assess engineered bacterial delivery systems, including gene circuit design, colonization control, biocontainment, and safety, and outline short-, medium-, and long-term milestones for clinical translation, cost-effectiveness, and intellectual property. The key takeaway is that precision microbiome medicine in CVD will require standardized assays, prospective validation, robust regulatory pathways, and equitable commercialization. By linking mechanistic insights with translational requirements, this review provides a framework for developing microbiome-targeted diagnostics and therapeutics in CVD.},
}

@article {pmid42865995,
year = {2026},
author = {Liu, F and Lv, Y and Wang, T and Li, C and Zhang, Y and Liu, L and Hu, X and Liang, Y and Zhu, F and Wang, J},
title = {Daily consumption of Fuzhuan brick tea improves lipid profile and vascular function associated with modulation in gut microbiota composition in healthy adults: a pilot randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1827773},
pmid = {42865995},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary strategies play a pivotal role in the prevention of cardiometabolic diseases. Animal studies have shown that Fuzhuan brick tea (FBT), a popular post-fermented tea, enhances cardiometabolic health by modulating the gut microbiota; however, there is no definitive evidence from human trials. This 12-week randomized controlled trial investigated the effects of FBT on the lipid profile, vascular function, and gut microbiota in healthy adults.

METHODS: This 12-week, open-label, parallel-group, randomized controlled trial was conducted in a rural community in northern China from September to November 2021. After giving informed consent, 120 healthy adults recruited were randomly assigned to either a group consuming two daily glasses of brewed FBT infusion (totaling 12 g/day) or a group consuming an equivalent amount of water. Serum lipid levels and vascular function, as indicated by flow-mediated dilation and nitroglycerin-mediated dilation, were measured at baseline (0 weeks) and 12 weeks after intervention. Fecal samples collected at baseline, 6 weeks, and 12 weeks underwent profiling of microbiota composition by shotgun metagenomic sequencing. This trial was completed and registered at chictr.org.cn (registration number ChiCTR2100047294).

RESULTS: Compared to water, consumption of FBT resulted in significantly reduced low-density lipoprotein cholesterol levels, with improved vascular function (the co-primary outcomes). The longitudinal metagenomic analysis detected no significant alterations in richness and distribution (alpha diversity). However, a subtle but statistically detectable shift in the gut microbiota composition (beta diversity) was observed. Exploratory species-level analyses suggested increases in bacteria that produce short-chain fatty acids, such as Roseburia hominis, Eubacterium saphenum, Eubacterium sp. AF15 50, Alistipes dispar, Blautia stercoris, and Lactobacillus amylolyticus, which were correlated with the lipid profile or vascular function.

CONCLUSION: Daily consumption of FBT demonstrated beneficial effects on lipid levels and vascular function in healthy adults, and was associated with exploratory shifts in gut microbiota composition, supporting FBT consumption is a simple, affordable, and practical dietary strategy for improving cardiometabolic health.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn/, identifier ChiCTR2100047294.},
}

@article {pmid42866017,
year = {2026},
author = {Herrera, G and Hua, X and Wu, Z and Liao, LM and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Gail, MH and Shi, J and Gierach, GL and Sinha, R and Vogtmann, E},
title = {Oral microbiome and postmenopausal breast cancer risk: findings from the NIH-AARP diet and health study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2728745},
pmid = {42866017},
issn = {2000-2297},
abstract = {INTRODUCTION: Breast cancer is the most frequently diagnosed cancer among women worldwide. Some case-control studies have reported associations between the oral microbiome and breast cancer, but the temporality of the association remains unclear. Therefore, we examined this association prospectively in the NIH-AARP Diet and Health Study.

METHODS: In 2005, oral wash samples were collected from a subset of the NIH-AARP cohort. We identified 318 women who developed breast cancer after collection and 318 controls, incidence-density matched on age at collection, race/ethnicity and smoking. DNA was extracted using the DNeasy PowerSoil Pro Kit, followed by shotgun metagenomic sequencing. Conditional logistic regression was used to calculate the odds ratios (OR) for associations between alpha- and beta-diversity and species- and gene-level metrics with breast cancer risk, adjusting for potential confounders.

RESULTS: Cases developed breast cancer on average 3.4 years after sample collection. Overall, the majority of the microbial metrics, including species and genes, showed largely null associations with the exception of Pielou's evenness (OR = 0.82; 95% CI = 0.70-0.95). When stratified by time to diagnosis, the inverse association with Pielou's evenness was only detected among women diagnosed within 2 years (29% of cases). In this subgroup, some previously reported associations, like the inverse association with the presence of Treponema (OR = 0.37; 95% CI = 0.17-0.78), were replicated. Null associations were predominantly observed for cases diagnosed more than 2 years after sample collection.

CONCLUSIONS: The oral microbiome was generally not prospectively associated with postmenopausal breast cancer in a US population and results suggested previous findings may reflect reverse causation.},
}

@article {pmid42866372,
year = {2026},
author = {Wei, Q and Li, Y and Ruan, A},
title = {A metagenomic snapshot of metabolic potentials in wintertime eutrophic sediments of Lake Taihu inferred from metagenome-assembled genomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929411},
pmid = {42866372},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding the metabolic potential of microbial communities in eutrophic lake sediments at the genome-resolved level is essential for predicting nutrient cycling and stress responses in contaminated freshwater ecosystems.

METHODS: In this study, we reconstructed 206 dereplicated metagenome-assembled genomes (MAGs) from sediment cores collected across four regions of Lake Taihu.

RESULTS: These dereplicated MAGs spanned 34 classified phyla and 72 classified genera, with 97.6% unclassified at the species level, indicating substantial genomic novelty. The cyanobacterial MAGs harbored diverse secondary metabolite biosynthetic gene clusters, suggesting a genomic basis for potential adaptive traits. Across all dereplicated MAGs, the highest biosynthetic potential for secondary metabolites was observed in Chloroflexota and Pseudomonadota. Putative antibiotic resistance genes were predominantly represented by glycopeptide resistance determinants (vanT/vanW) and resistance-nodulation-division (RND) efflux pumps, which together accounted for 86.1% of the detected resistome. Additionally, 490 predicted horizontal gene transfer (HGT) events were identified, with transferred genes being most prevalent in energy metabolism (12.4%), translation (10.8%), and transcriptional regulation (7.2%).

DISCUSSION: This genome-resolved survey provides a foundation for understanding the metabolic and genomic potential of sediment microbiomes in eutrophic freshwater systems.},
}

@article {pmid42866455,
year = {2026},
author = {de Aguiar, LS and Echeverria, LS and Genaro, LM and Rodrigues, BAG and de Paula Pessoa Bezerra, M and Costa, FO and Pascoal, LB and de Sene Portel Oliveira, P and de Lourdes Setsuko Ayrizono, M and Leal, RF},
title = {Gut microbiota profile and response to neoadjuvant chemoradiotherapy in patients with rectal cancer: a systematic review.},
journal = {Translational gastroenterology and hepatology},
volume = {11},
number = {},
pages = {111},
pmid = {42866455},
issn = {2415-1289},
abstract = {BACKGROUND: Rectal cancer (RC) accounts for approximately 30% of all colorectal cancers, with pathological complete response (pCR) rates following neoadjuvant chemoradiotherapy (nCRT) ranging from 10-15% and reaching up to 38% with total neoadjuvant therapy. The intestinal microbiota has emerged as a potential modulator of treatment efficacy, offering opportunities for patient stratification and personalized therapy. This review aimed to the best of our knowledge, no robust systematic review has focused on the microbiota profile as a biomarker of response to nCRT in RC. Most studies focus on the effect of the microbiota on the adjuvant response to chemotherapy. To synthesize the available evidence and fill the gap in knowledge on the role of the intestinal microbiota in modulating treatment response and prognosis in patients with RC undergoing nCRT.

METHODS: This systematic review was registered in PROSPERO (CRD420251174787). A comprehensive search was conducted across PubMed, PubMed Central (PMC), Virtual Health Library (BVS), Scopus, Web of Science, Embase, and Cochrane Library. Studies evaluating the association between the intestinal microbiota and treatment response or prognosis in adult patients with RC were included. Two independent reviewers selected studies, and data were extracted from eligible studies.

RESULTS: Seventeen studies were included, all published after 2020, with 11 published between 2023 and 2025. Most studies originated from China (11/17). Sequencing methodologies included 16S rRNA sequencing (9 studies), shotgun metagenomics (6 studies), RNA-sequencing (2 studies), and whole-exome sequencing with Path-seq (1 study). A total of 868 patients were evaluated. Alpha-diversity did not differ significantly between responders and non-responders in most studies. Beta-diversity results were heterogeneous. Responders were associated with genera such as Bacteroides, Campylobacter, Faecalibacterium, and Lactobacillus, while non-responders showed enrichment of Akkermansia, Streptococcus, and Prevotella. Functional pathway analyses revealed that responders showed enrichment in pathways related to anaerobic energy metabolism, amino acid synthesis, and innate immune activation [cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway], whereas non-responders showed enrichment of fatty acid metabolism and anti-apoptotic pathways. Nine studies developed predictive models with AUC values ranging from 0.707 to 0.980.

CONCLUSIONS: The intestinal microbiota may play a relevant role in modulating response to nCRT in RC, particularly through functional metabolic pathways rather than taxonomic composition alone. Predictive models based on microbial signatures show promising accuracy, although standardization of methodologies and validation in diverse populations are needed before clinical implementation.},
}

@article {pmid42866779,
year = {2026},
author = {Wei, Z and Wang, X and Lv, J and Cheng, Y},
title = {Progress of machine perfusion in managing donor-derived infections in liver transplantation.},
journal = {Translational gastroenterology and hepatology},
volume = {11},
number = {},
pages = {115},
pmid = {42866779},
issn = {2415-1289},
abstract = {Donor-derived infection (DDI), particularly when involving multidrug-resistant organisms (MDROs), represents a formidable barrier in liver transplantation, contributing significantly to high graft discard rates amid the global organ shortage. Conventional static cold storage (SCS) remains inadequate for infected grafts, as it lacks the capacity for dynamic functional assessment or targeted therapeutic intervention, frequently necessitating the exclusion of these high-risk organs. Machine perfusion (MP) has emerged as a transformative strategy, preserving liver grafts under physiological conditions while effectively mitigating ischemia-reperfusion injury (IRI). Beyond its preservation benefits, the integration of antibiotic therapy into MP platforms facilitates a conceptual shift toward active ex vivo pharmacologic decontamination. By leveraging continuous vascular flow, MP enhances intrahepatic antibiotic delivery efficiency and distribution uniformity, creating a potent anti-infective barrier that suppresses microbial proliferation and reduces pathogen-induced inflammation, all while avoiding the systemic toxicity associated with conventional drug administration. Despite this promise, clinical implementation faces hurdles, including the absence of standardized perfusion protocols, delayed diagnostic turnaround times, and concerns regarding potential hepatotoxicity from high-dose antibiotics. Future progress hinges on the integration of rapid diagnostic technologies like metagenomic sequencing and the development of novel anti-infective agents. Ultimately, precision antimicrobial management via MP offers a viable pathway to transform infection-exposed livers from marginal to safely transplantable resources, thereby expanding the donor pool and improving recipient outcomes.},
}

@article {pmid42866952,
year = {2026},
author = {Larralde, M and Blom, J and Gourlé, H and Radoykova, HS and Paoli, L and Zeller, G and Carroll, LM},
title = {Fast, flexible gene cluster family delineation with IGUA.},
journal = {Nucleic acids research},
volume = {54},
number = {19},
pages = {},
doi = {10.1093/nar/gkag975},
pmid = {42866952},
issn = {1362-4962},
support = {KAW 2020.0239//SciLifeLab & Wallenberg Data Driven Life Science (DDLS)/ ; 2023-05212//Swedish Research Council/ ; //EMBL/ ; //LUMC/ ; SFB 1371//German Research Foundation/ ; 395357507//Deutsche Forschungsgemeinschaft/ ; ERC-2023-SyG-101118531/ERC_/European Research Council/International ; //EPFL School of Life Sciences/ ; //Oak foundation/ ; //Promex Stiftung für die Forschung/ ; //Swiss Government Excellence Scholarship/ ; //Laura Carroll's KAW/ ; //Umeå University/ ; },
mesh = {*Multigene Family ; Clustering Algorithms ; *Genomics/methods ; *Software ; Genome, Bacterial ; Cluster Analysis ; },
abstract = {Prokaryotic genomes harbor a variety of functional elements encoded as contiguous multi-gene clusters. To identify homologous gene clusters, computational tools that account for multi-gene architectures are needed to group gene clusters into Gene Cluster Families (GCFs). However, existing GCF delineation methods do not scale well to large datasets and are often limited to certain subclasses of gene clusters. Here, we present IGUA (Iterative Gene clUster Analysis; https://github.com/zellerlab/IGUA), a scalable, flexible GCF delineation method for genomic segments with multi-gene architectures. On a biosynthetic gene cluster (BGC) clustering task, IGUA is 29× and 10× faster than the state-of-the-art (BiG-SCAPE v2 and BiG-SLiCE v2, respectively; 28 CPUs), without sacrificing accuracy. To highlight its scalability, we use IGUA to cluster >2.8 million BGCs from ≈1 million prokaryotic genomes in <18 h (n = 2 829 071 BGCs to 56 960 GCFs). To showcase its utility beyond BGC clustering, we use IGUA to cluster five additional prokaryotic gene cluster types (secretion systems, prophages, genomic islands, phage-plasmids, and carbohydrate active enzyme [CAZyme] gene clusters). Overall, IGUA represents a versatile GCF delineation tool with unmatched computational efficiency and flexibility, enabling (meta)genomic mining applications at unprecedented scales.},
}

*Multigene Family
Clustering Algorithms
*Genomics/methods
*Software
Genome, Bacterial
Cluster Analysis

@article {pmid42867185,
year = {2026},
author = {Jang, S and Yang, H and Lee, S and Kim, P and Yun, BS and Kim, D and Ryu, CM},
title = {Silicate fertilizer mitigates methane emissions from rice paddies by enriching Burkholderia to modulate microbial interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag255},
pmid = {42867185},
issn = {1751-7370},
abstract = {Methane emissions from rice paddies are a major source of greenhouse gases, and silicate fertilizer (SF) derived from blast furnace slag has emerged as an environmentally friendly amendment that reduces methane release. SF modifies the soil redox environment by supplying electron acceptors such as iron, but the microbial mechanisms underlying methane mitigation remain unclear. Here, we combined metagenomic profiling, microbial isolation, and greenhouse experiments to show that SF consistently enriched Burkholderia vietnamiensis together with the methanotrophs in the rice rhizosphere. Inoculation of B. vietnamiensis strain HU01 alone reproduced the methane-suppressing effect of SF and increased methanotroph abundance. Cell-free culture supernatants of HU01 stimulated the growth of Methylococcus geothermalis and Methylocystis parvus through secreted, low-molecular-weight, heat-stable metabolites. Although metabolic modeling predicted primary metabolites such as L-glutamate and cobalamin as candidate cross-feeding factors, LC-MS/MS analysis of the highly active fractions indicated that the robust bioactivity was primarily driven by a chemically complex metabolite mixture rather than these ubiquitous single compounds. These results provide direct evidence that enrichment of a single heterotrophic species can enhance methane oxidation by stimulating methanotroph activity through metabolite exchange. B. vietnamiensis HU01 represents a promising microbial resource for methane mitigation and illustrates how targeted heterotroph-methanotroph interactions can be leveraged for climate-smart rice cultivation.},
}

@article {pmid42867261,
year = {2026},
author = {Wang, X and Wang, H and Yang, J and Chen, H and Liu, X and Chen, X and Liao, L and Dong, Y and Yu, L and Xiu, Z and Yang, Y},
title = {Metagenome-assembled genomes of four psychrotolerant Clostridium-affiliated bacteria from an Fe(III)-reducing enrichment culture of Antarctic penguin-impacted soil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085426},
doi = {10.1128/mra.00854-26},
pmid = {42867261},
issn = {2576-098X},
abstract = {We report four Clostridium-affiliated metagenome-assembled genomes (MAGs) recovered from a psychrotolerant enrichment culture capable of Fe(III) reduction at 4°C, seeded from Antarctic penguin-impacted soil. The four MAGs ranged from 3.6 to 5.3 Mb in size, with G + C contents of approximately 31.0% and estimated genome completeness ranging from 82.76% to 98.54%.},
}

@article {pmid42868780,
year = {2026},
author = {Lin, W and Ding, Y and Ren, H and Wang, Y},
title = {Co-expression of alnA and bphC in alfalfa enhances PCB phytoremediation by coupling bioavailability modulation and intracellular detoxification.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143851},
doi = {10.1016/j.jhazmat.2026.143851},
pmid = {42868780},
issn = {1873-3336},
abstract = {Phytoremediation of polychlorinated biphenyls (PCBs)-contaminated soils is hindered by low PCB bioavailability and insufficient plant detoxification. Here, we engineered transgenic alfalfa co-expressing alnA (encoding an emulsifying protein) and bphC (encoding a ring-cleavage dioxygenase) to address these barriers. Five representative congeners spanning a range of chlorination degrees were selected to evaluate the system's efficacy. The transgenic AB lines achieved sustained rhizosecretion of AlnA, enhancing PCB solubility by 2.0- to 3.2-fold relative to wild-type (WT) plants. While enhanced bioavailability typically exacerbates phytotoxicity, endogenous BphC cleaved the biphenyl ring, preventing toxic intermediate accumulation. This extracellular solubilization-intracellular detoxification synergy enabled AB alfalfa to maintain improved growth under PCB stress, increasing root accumulation by 3.7-fold and overall removal by 2-fold compared to WT alfalfa. Metagenomic and structural equation modeling revealed that while microbial genes act as "proximate executors" directly degrading PCBs, the transgenic plant functions as the "primary driver". The AB lines enriched specific degraders (Pseudomonas and certain genera within the order Burkholderiales) and assembled a functional network for aerobic PCB degradation. This integrated plant-microbiome system offers a low-maintenance strategy for in situ remediation of PCB-contaminated sites.},
}

@article {pmid42859003,
year = {2026},
author = {Dong, L and Luo, S and Misbahullah, SM and Xu, J and Wan, S and Gao, H and Qin, Z},
title = {Polymerization-dependent gut microbiome responses to curdlan β-1,3-glucan and its oligosaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120524},
doi = {10.1016/j.foodres.2026.120524},
pmid = {42859003},
issn = {1873-7145},
mesh = {*beta-Glucans/metabolism/chemistry ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Feces/microbiology ; *Oligosaccharides/metabolism/chemistry ; Polymerization ; Fermentation ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {β-1,3-Glucan is a dietary fiber with microbiome-modulating potential, yet the role of polymerization degree on microbial composition and metabolism remains unclear. Curdlan is an insoluble linear β-1,3-glucan widely used as a food hydrocolloid that provides a model to examine structure-dependent microbiome responses. We compared glucose, curdlan (CBG), and curdlan-derived β-1,3-glucan oligosaccharides (OBG) using anaerobic in vitro fermentation of pooled human feces. A multi-omics approach integrating 16S rRNA sequencing, shotgun metagenomics, short-chain fatty acid (SCFA) quantification, and untargeted metabolomics was applied to resolve taxonomic, functional, and metabolic shifts. Both CBG and OBG enriched Bacteroidota and enhanced carbohydrate metabolism relative to glucose, but through distinct pathways. CBG promoted polymer-associated carbohydrate processing, with enrichment of β-1,3-glucan-degrading enzymes such as GH16, Sus-like transport systems, and polysaccharide-specialized taxa (e.g., Prevotella and Bifidobacterium), and butyrate production. In contrast, OBG favored transporter-mediated substrate uptake, broader microbial participation (e.g. Parabacteroides and Enterobacteriaceae), and a metabolite profile enriched in amino acid-derived compounds and branched-chain SCFAs. These findings demonstrate that β-1,3-glucan polymerization degree governs microbiome functional routing and highlight polymerization degree as a tunable parameter for designing microbiome-directed carbohydrate ingredients with predictable metabolic outcomes.},
}

*beta-Glucans/metabolism/chemistry
Humans
*Gastrointestinal Microbiome/drug effects/physiology
Feces/microbiology
*Oligosaccharides/metabolism/chemistry
Polymerization
Fermentation
Dietary Fiber/metabolism
Fatty Acids, Volatile/metabolism
Glucose/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42859015,
year = {2026},
author = {Yu, Z and Wang, W and Chen, F and Li, L and Luo, L and Zhong, X and Liu, D and Tang, W and Liu, X and Huang, M},
title = {Temporal dynamics and metabolic potential of microbial dark matter during dry storage of high-temperature Daqu revealed by metagenome-assembled genomes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120539},
doi = {10.1016/j.foodres.2026.120539},
pmid = {42859015},
issn = {1873-7145},
mesh = {*Metagenome ; *Alcoholic Beverages/microbiology/analysis ; *Hot Temperature ; Fermentation ; *Food Microbiology ; Metagenomics ; *Food Storage/methods ; Bacillota/genetics/metabolism ; Archaea/genetics/metabolism ; *Microbiota/genetics ; },
abstract = {High-temperature Daqu is the core starter culture for Jiang-flavor Baijiu production, whose microbial community directly shapes the enzymatic properties and flavor precursor profiles of fermentation systems. Dry storage drives microbial succession and functional maturation of Daqu, yet existing studies have predominantly focused on cultivable and well-characterized taxa, leaving the temporal dynamics and metabolic contributions of microbial dark matter (MDM) largely unexplored at the genome-resolved level. Using genome-resolved metagenomics, we reconstructed 52 medium- to high-quality metagenome-assembled genomes (MAGs) from high-temperature Daqu samples across a six-month dry storage period and identified five novel unclassified MDM lineages comprising four Bacillota-affiliated bacterial lineages and one archaeal lineage. Comparative genomic analysis revealed distinct functional differentiation between MDM lineages and dominant culturable taxa, as MDM lineages were enriched in genes associated with carbohydrate uptake and fermentative acid production and harbored a streamlined biosynthetic gene cluster (BGC) profile with uniformly high sequence novelty. Temporal dynamic analysis showed that MDM lineages from different storage microhabitats exhibited divergent succession patterns, and conventional physicochemical parameters showed limited explanatory power for MDM community variation, with only glucoamylase activity displaying a marginal association trend. This study provides genome-resolved insights into uncultured MDM lineages during high-temperature Daqu dry storage, expands the genomic repertoire of uncultured microbiota in traditional fermentation ecosystems, and offers novel perspectives for deciphering Daqu maturation mechanisms and quality regulation.},
}

*Metagenome
*Alcoholic Beverages/microbiology/analysis
*Hot Temperature
Fermentation
*Food Microbiology
Metagenomics
*Food Storage/methods
Bacillota/genetics/metabolism
Archaea/genetics/metabolism
*Microbiota/genetics

@article {pmid42859016,
year = {2026},
author = {Ji, Q and Qu, H and Chen, D and Li, Q and Zong, L and Liu, Y and Huang, Y and Gu, R},
title = {Matrix-associated spatial structure contributes to compositional stability of a complex multispecies starter culture under microbial perturbation: Insights from kefir grains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120540},
doi = {10.1016/j.foodres.2026.120540},
pmid = {42859016},
issn = {1873-7145},
mesh = {*Kefir/microbiology ; Fermentation ; *Food Microbiology/methods ; *Microbiota ; Cultured Milk Products/microbiology ; },
abstract = {Complex multispecies starter cultures can enrich the metabolic and sensory diversity of fermented foods, but industrial use is limited by compositional drift, overgrowth of dominant taxa, and vulnerability to exogenous microbial contamination. Kefir grains (KG), a matrix-encapsulated complex starter culture with stable serial propagation, provide a model for how spatial structure contributes to starter stability. We compared matrix-associated KG with free kefir-fermented milk (FKFM), representing a grain-free liquid-phase kefir microbial community, under a large-scale microbial challenge. During the acute 24 h challenge, target-taxon drift estimated from PMA-qPCR data was lower in KG than in the liquid compartments. Ten-generation serial transfer caused stronger community restructuring and Shannon diversity loss in FKFM, whereas KG showed constrained compositional adjustment and remained relatively clustered in Bray-Curtis ordination space. Species-level metagenomic tracking showed broader expansion, retention, and cumulative drift of species-level signals corresponding to exogenous challenge strains in FKFM, while more of these signals in KG followed restricted/stable trajectories. Kefir cell-free supernatant inhibited multiple challenge strains beyond the effect of low pH, indicating a contribution of diffusible inhibitory factors. SEM and live/dead staining revealed rough matrix-associated surfaces and heterogeneous cell states in KG. Together, the results support a model in which spatial structure, prior niche occupancy, and diffusible inhibition jointly contribute to the compositional stability and anti-perturbation capacity of this complex starter culture, informing the design of spatially structured synthetic starter consortia for industrial fermentation.},
}

*Kefir/microbiology
Fermentation
*Food Microbiology/methods
*Microbiota
Cultured Milk Products/microbiology

@article {pmid42859679,
year = {2026},
author = {Patsakis, M and Provatas, K and Mouratidis, I and Georgakopoulos-Soares, I},
title = {Derivation of oligonucleotide barcodes that are absent from natural sequences.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag251},
pmid = {42859679},
issn = {2635-0041},
abstract = {DNA barcodes are short synthetic sequences used to uniquely identify target molecules, samples, or objects, and are essential for a wide range of biotechnology applications including high-throughput sequencing, lineage tracing, genetic screens, massively parallel reporter assays, and DNA-based data storage. However, randomly generated barcodes are prone to off-target hybridization and cross-reactivity with endogenous biological sequences, which can compromise experimental specificity and interpretation. Barcodes derived from sequences that are entirely absent from natural genomes, termed DNA primes, offer an ideal solution by eliminating the possibility of unintended interactions with biological material. Here, we present barcodesDB, a comprehensive database of synthetic DNA barcodes systematically identified by scanning 403 199 complete organismal genome assemblies across the tree of life, together with 215 Gbp of raw metagenomic sequencing reads spanning marine, soil, polar and host-associated environments. These barcodes are absent, on either strand, from every assembly and sequencing read examined in the release described, providing maximal specificity and minimizing cross-reactivity for downstream applications. We provide an open-access web application that enables researchers to search for barcodes satisfying user-defined constraints, including GC content and substring requirements, and to query whether candidate sequences occur in nature. This resource supports robust and scalable barcode design for diverse experimental and applied contexts. Our database is publicly available at: https://barcodesdb.com/.},
}

@article {pmid42859685,
year = {2026},
author = {Chatzigiannidou, I and Taparia, T and Johansen, PL and Berzina, L and Nesme, J and Petersen, M and Sørensen, SJ and Brix, S and Kristiansen, K},
title = {Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag268},
pmid = {42859685},
issn = {2730-6151},
abstract = {Agricultural soils harbor highly diverse and functionally rich microbial communities, yet much of their genomic potential remains unexplored. Here, we present a genome-resolved metagenomic analysis of 455 soil samples collected at different depths and seasonal stages across two Danish agricultural fields representing sandy and clay soil types. Ultra-deep shotgun sequencing enabled the recovery of 58 831 medium to high-quality prokaryotic metagenome-assembled genomes (MAGs), which were dereplicated into 56 340 strain-level MAGs and 9090 species-level genome bins (SGBs) spanning 49 prokaryotic phyla. The majority of the SGBs represented previously uncharacterized species. Functional annotation revealed extensive biosynthetic and metabolic potential, including 46 913 biosynthetic gene clusters and prevalent genes linked to nitrogen cycling. Notably, 378 MAGs harbored the nitrous oxide reductase gene nosZ. Soil type and depth strongly influenced microbial diversity and functional traits. These findings provide a resource for linking microbial traits to soil function of potential value for better sustainable agricultural practice.},
}

@article {pmid42859709,
year = {2026},
author = {de Bruijn, TEP and Doekes, HM and Kupczok, A},
title = {Temperate versus virulent phage lifestyle impacts microdiversity in soil environments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag265},
pmid = {42859709},
issn = {2730-6151},
abstract = {Bacteriophages are not only the most ubiquitous biological entity on earth, but they also display remarkable genetic diversity across and within populations. While macrodiversity has been extensively studied, the drivers of microdiversity (intra-species genetic diversity) remain poorly understood, particularly in relation to phage lifestyle. The distinguishing ability of temperate phages to integrate themselves into the host genome has an unknown influence on the microdiversity present. This difference in microdiversity could impact the adaptability of phages to (a)biotic factors. To identify a possible association between microdiversity and lifestyle, we analysed 12 existing viromics datasets focusing on soil bacteriophages, including 43 171 viral genomes in total. We found that phages predicted to be temperate consistently exhibit higher microdiversity than their virulent counterparts in 8 of 12 datasets. Of the remaining four datasets, one showed the opposite trend and three datasets did not show a significant trend at all. The detected pattern holds across multiple quality thresholds and lifestyle prediction methods. These findings suggest that lifestyle has a significant impact on genetic variation within phage populations, with potential implications for phage-host coevolution and environmental adaptability.},
}

@article {pmid42860091,
year = {2026},
author = {Chen, S and Xin, X and Yang, J and Xu, H and Zhu, X and Wang, G and Yan, W},
title = {Conductive Fe3O4 drives a stress-dependent shift in electron-transfer strategies during anaerobic tetramethylammonium hydroxide degradation.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127060},
doi = {10.1016/j.watres.2026.127060},
pmid = {42860091},
issn = {1879-2448},
abstract = {Anaerobic treatment of tetramethylammonium hydroxide (TMAH) wastewater is often constrained by metabolic disruption under high TMAH loading. Conductive Fe3O4 has shown promise for enhancing anaerobic bioprocesses; however, the dominant mechanism governing its enhancement under different metabolic conditions remains unclear. Here, anaerobic reactors were operated under stepwise increases in TMAH concentration (1-10 g/L) to compare the effects of soluble Fe[2+] and conductive Fe3O4 using reactor performance, electrochemical characterization, intracellular reducing-equivalent measurements, and integrated metagenomics and metatranscriptomics analyses. At low-to-moderate TMAH loadings (1-5 g/L), Fe3O4 and Fe[2+] exhibited comparable improvements in TMAH degradation and methane production, together with elevated soluble Fe[2+] and reduced ferredoxin, indicating that dissolved iron was the dominant contributor. Under severe TMAH stress (10 g/L), both iron amendments improved reactor performance, whereas Fe3O4 became markedly more effective than Fe[2+], achieving complete TMAH removal and over twofold higher methane production than the unamended control. Electrochemical analyses showed that Fe3O4 enhanced extracellular electron-transfer activity, accompanied by intensified riboflavin-like redox signals. Integrated metagenomic and metatranscriptomic analyses further revealed concurrent enrichment of electroactive bacteria and syntrophic methanogens, together with increased transcription of genes involved in intracellular electron metabolism, particularly those associated with F420-dependent C1 metabolism and HdrABC-MvhADG-mediated electron bifurcation. Collectively, these findings unravel a stress-dependent transition in the mechanism underlying Fe3O4 enhancement, from dissolved-iron-supported intracellular reducing-equivalent metabolism under low-to-moderate TMAH loadings to conductivity-associated coordination between extracellular electron transfer and intracellular methanogenic metabolism under severe TMAH stress. This mechanistic insight provides a basis for optimizing conductive iron mineral-assisted anaerobic treatment of high-strength TMAH wastewater.},
}

@article {pmid42860095,
year = {2026},
author = {Ju, H and Yuan, Y and Jiang, L and Song, C and Li, J and Zou, S and Korir, RK and Gin, KY and Zhang, J},
title = {Winter ice regulates antibiotic resistance dynamics through seasonal genetic reservoirs across lake compartments.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127053},
doi = {10.1016/j.watres.2026.127053},
pmid = {42860095},
issn = {1879-2448},
abstract = {Antibiotic resistance is a growing environmental and public-health threat, yet its seasonal dynamics in cold-region freshwater ecosystems remain poorly understood. Using year-round observations, metagenomic sequencing, and machine learning, we investigated antibiotic resistance genes (ARGs) across ice, water, and sediment in an ice-covered lake. Winter ice contained significantly higher abundances of ARGs, mobile genetic elements (MGEs), and microbial hosts than water and sediments. Driver analysis based on explainable machine learning showed that ARG dynamics in ice were primarily associated with MGEs, whereas ARGs in water and sediments were associated with host-related ecological processes and environmental conditions. During spring, ice-associated ARGs, MGEs, and their microbial hosts showed potential contribution to the water column, expanding resistance-risk hotspots and reorganizing associations among ARGs, MGEs, hosts, and virulence factors. These findings indicate that winter ice acts as a seasonal reservoir of antibiotic resistance, regulating spring antibiotic resistance dynamics and potential health risks.},
}

@article {pmid42860401,
year = {2026},
author = {Xu, Z and Jiang, H and Huang, W and Chan, A and Lin, Y and Chan, T and Lui, RN and Wong, MTL and Mak, JWY and Chan, FKL and Chevarin, C and Colombel, JF and Buisson, A and Ng, SC},
title = {Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42860401},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/therapy/microbiology ; Pilot Projects ; *Fecal Microbiota Transplantation/methods/adverse effects ; Female ; *Escherichia coli/genetics/physiology ; Male ; Feces/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli Infections/therapy/microbiology ; Young Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {Adherent-invasive Escherichia coli (AIEC) is implicated in Crohn's disease (CD) pathogenesis, but whether fecal microbiota transplantation (FMT) clears mucosal AIEC and alters fecal and mucosal microbiomes has not been studied. In this open-label pilot study, thirty adults with CD and seropositivity for serum anti-E.coli antibody (AEcAb) received a single colonoscopic FMT from one of two donors (ClinicalTrials.gov identifier NCT05611866). The primary outcome was adverse events (AEs) within 12 weeks after FMT; secondary outcomes included changes in mucosal AIEC, clinical measures, and fecal and mucosal microbiome profiles. Shotgun metagenomic sequencing for fecal samples and 16S rRNA sequencing for ileal mucosal samples were performed at baseline and after FMT. Baseline AEcAb levels were higher in patients with mucosal AIEC colonization (p = 0.019) and remained elevated after FMT. No FMT-related serious adverse events were reported. FMT was associated with mucosal AIEC decolonization in all 8 evaluable baseline-positive patients. Mucosal alpha diversity increased after FMT (p = 0.023), which correlated with reduced fecal calprotectin (p = 0.034). Microbial pathway profiles in CD patients resembled those of their respective donors with reduced donor-recipient dissimilarity post-FMT (p = 0.030), particularly among recipients with mucosal AIEC decolonization (p = 0.039). In conclusion, this open-label pilot study demonstrates the feasibility of FMT for modulating mucosal AIEC colonization in CD and highlights the importance of capturing microbial changes at the disease site that may be undetectable in fecal samples.},
}

Humans
*Crohn Disease/therapy/microbiology
Pilot Projects
*Fecal Microbiota Transplantation/methods/adverse effects
Female
*Escherichia coli/genetics/physiology
Male
Feces/microbiology
Adult
*Intestinal Mucosa/microbiology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Escherichia coli Infections/therapy/microbiology
Young Adult
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid42860710,
year = {2026},
author = {McAleese, K and Vather, M and Vargas, SO and Sharma, TS and Elisofon, SA and Guenther, G},
title = {Successful Liver Transplantation in a Child With Invasive Aspergillus terreus Cholangitis Identified via Plasma Metagenomic Next-Generation Sequencing.},
journal = {Pediatric transplantation},
volume = {30},
number = {10},
pages = {e70490},
doi = {10.1111/petr.70490},
pmid = {42860710},
issn = {1399-3046},
mesh = {Humans ; *Liver Transplantation ; Female ; *Cholangitis/microbiology/surgery/diagnosis ; *Aspergillus/genetics/isolation & purification ; *Biliary Atresia/surgery ; High-Throughput Nucleotide Sequencing ; *Aspergillosis/diagnosis/surgery ; Child, Preschool ; Metagenomics ; *Postoperative Complications/diagnosis/surgery/microbiology ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; Portoenterostomy, Hepatic ; },
abstract = {BACKGROUND: Ascending cholangitis, one of the most common complications in patients with biliary atresia (BA) after Kasai hepatoportoenterostomy (HPE), impacts native liver survival. Typically, enteric bacterial flora are the source of infection, and fungal infections of the biliary tree are rare.

CASE REPORT: We report the case of a 3-year-old female with BA status post Kasai HPE who developed Aspergillus terreus cholangitis (complicated by hepatic vein thrombus) identified through plasma metagenomic next-generation sequencing (NGS) of microbial cell-free deoxyribonucleic acid (DNA). Despite improvement in galactomannan (GM) antigen indices while on antifungal therapy with voriconazole and anticoagulation, she experienced complications with the extension of septic thrombus and persistent cholestasis; thrombus tissue sampling later confirmed the diagnosis and antimicrobial sensitivities. Ultimately, native liver explantation succeeded in achieving source control with sustained normalization of GM indices after the completion of voriconazole. Post-transplant, she received routine immunosuppression and infection prophylaxis per institutional protocol and remains well without infectious complications more than 1 year later.

DISCUSSION: This case highlights the important role of newer molecular diagnostic tools in facilitating timely species-level pathogen identification and initiation of targeted therapy (in this case, 35 days prior to confirmed tissue diagnosis), particularly in circumstances where the risk-to-benefit ratio of invasive tissue sampling is unfavorable. Despite the significant morbidity associated with invasive fungal infection, transplantation followed by standard immunosuppression is a reasonable therapeutic option with successful outcomes in patients who are otherwise suitable transplant candidates.},
}

Humans
*Liver Transplantation
Female
*Cholangitis/microbiology/surgery/diagnosis
*Aspergillus/genetics/isolation & purification
*Biliary Atresia/surgery
High-Throughput Nucleotide Sequencing
*Aspergillosis/diagnosis/surgery
Child, Preschool
Metagenomics
*Postoperative Complications/diagnosis/surgery/microbiology
Antifungal Agents/therapeutic use
Voriconazole/therapeutic use
Portoenterostomy, Hepatic

@article {pmid42861590,
year = {2026},
author = {Deng, LR and Zhong, YM and Zhu, SF and Wu, ZY and Chen, FJ and Huang, CY and Wu, QY and Tomlinson, B and Tan, HE and Li, YH},
title = {Anemoside B4 from Pulsatilla chinensis Ameliorates Ulcerative Colitis by Inhibiting Inflammatory Responses via the Modulation of the Gut Microbiota-Immune Interplay.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-29},
doi = {10.1142/S0192415X26500849},
pmid = {42861590},
issn = {1793-6853},
abstract = {We previously demonstrated that anemoside B4 (AB4) exerts a beneficial effect in a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis (UC). In this study, we further explored the mechanism of AB4 against UC from the perspective of gut microbiota-immune interplay. The gut microbiota was depleted in two DSS-induced colitis models to investigate the modulatory effects of the gut microbiome on immune responses and the activity of AB4. In parallel, adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1-deficient (Rag1[-/-]) mice was used to elucidate the alterations in the gut microbiota associated with immune-mediated colitis as well as the modulation by AB4. qPCR, ELISA and western blotting were used to determine the inflammatory responses of mice with colitis, while immunohistochemistry and flow cytometry were employed to determine the CD4[Formula: see text] T cell function and the underlying mechanism. Metagenomic sequencing analysis was used to detect changes in the intestinal microbiota. The depletion of the gut microbiota attenuated disease severity and immune responses in mice with DSS-induced acute and chronic colitis. Notably, the inhibitory effects of orally administered AB4 on colitis progression and immune responses were abrogated. In addition, colitis induced by adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1[-/-] mice was accompanied by CD4[Formula: see text] T cell engraftment and alterations in gut microbiota. Remarkably, all these pathological changes were significantly attenuated by AB4. Crucially, we found that AB4 suppresses the proliferation, migration, and differentiation of CD4[Formula: see text] T cells, which provides a mechanistic basis for its immunosuppressive effects. Collectively, these findings indicate that the gut microbiota and the immune system, particularly CD4[Formula: see text] T cells, interact with each other in the initiation of colitis. We show that, by targeting this gut microbiota-immune interplay, AB4 is a promising therapeutic strategy for UC.},
}

@article {pmid42861600,
year = {2026},
author = {Liu, Y and Ning, X and Liu, Y and Yu, Z and Liu, J and Xu, X and Zhao, J and Sun, S},
title = {Potential Roles of Escherichia coli in IgA Nephropathy: Evidence, Mechanistic Hypotheses and Microbiota-Targeted Strategies.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70455},
doi = {10.1111/1751-7915.70455},
pmid = {42861600},
issn = {1751-7915},
support = {82470735//National Natural Science Foundation of China/ ; 2023TD-02//Shaanxi Provincial Health Commission/ ; 2023-ZDLSF-15//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLSF03-12//Key Research and Development Projects of Shaanxi Province/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/therapy/pathology ; *Escherichia coli/pathogenicity ; Animals ; *Gastrointestinal Microbiome ; Immunoglobulin A/metabolism ; },
abstract = {IgA nephropathy (IgAN), the most common primary glomerular disease, involves mucosa-kidney axis dysregulation, with gut dysbiosis increasingly implicated in its pathogenesis. Certain Escherichia coli (E. coli) strains harbour virulence-associated features that promote intestinal colonization, barrier disruption and immune activation. Recent microbiome and metagenomic studies have reported an enrichment of E. coli in patients with IgAN, suggesting a potential link to the mucosa-kidney axis. Nevertheless, E. coli may contribute to IgAN through two major pathways. First, sustained LPS exposure may induce aberrant production of galactose-deficient IgA1 (Gd-IgA1) by stimulating B cells and activate the NLR family pyrin domain containing 3 (NLRP3) inflammasome in macrophages, thereby amplifying systemic and renal inflammation. Second, metabolic reprogramming is associated with increased circulating sphingosine-1-phosphate (S1P) and altered production of indole and trimethylamine (TMA); S1P may promote mesangial proliferation and fibrosis, whereas indole- and TMA-related pathways may contribute to tubulointerstitial injury and chronic kidney disease (CKD) progression. Beyond conventional gut microbiota-targeted interventions, emerging precision therapeutic strategies offer promising new directions for the etiological treatment of IgAN. This review summarizes E. coli virulence factors, pathogenesis, and host, environmental, and ecological factors driving its gut expansion in IgAN patients and outlines corresponding therapeutic strategies.},
}

Humans
*Glomerulonephritis, IGA/microbiology/therapy/pathology
*Escherichia coli/pathogenicity
Animals
*Gastrointestinal Microbiome
Immunoglobulin A/metabolism

@article {pmid42861963,
year = {2026},
author = {Xie, P and Luo, M and Fan, J and Xiong, L},
title = {A global atlas of the gut virome reveals subtype-specific and functional alterations in irritable bowel syndrome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0090126},
doi = {10.1128/msystems.00901-26},
pmid = {42861963},
issn = {2379-5077},
abstract = {The gut virome is a critical component of the microbiome-gut-brain axis; however, its role in irritable bowel syndrome (IBS) remains poorly understood due to limited sample sizes and geographic bias. We aimed to construct a comprehensive global atlas of the IBS gut virome to elucidate its composition, functional potential, and clinical relevance across diverse populations and IBS subtypes. We integrated multi-cohort data comprising 1,104 samples (790 IBS patients and 314 healthy controls) from 11 cohorts across 10 geographic regions. A standardized bioinformatic pipeline was employed to perform viral mining from metagenomic and virus-like particle-enriched metaviromic data. The IBS virome exhibited significant taxonomic alterations, with specific viral signatures distinguishing IBS-D, IBS-C, and IBS-M subtypes. Geographic region was identified as a significant factor influencing the viral community structure. Functionally, the IBS virome was enriched in auxiliary metabolic genes involved in carbon metabolism and neurotransmitter precursor synthesis (histidine and tryptophan metabolism), as well as a distinct profile of virulence factors and antibiotic resistance genes. Furthermore, in a specific cohort, certain viral taxa were significantly correlated with the severity of anxiety and depression. Machine learning models based on viral signatures achieved robust performance for IBS subtyping (area under the curve = 0.92). This study establishes a global baseline for the IBS gut virome, demonstrating that viral communities are dynamically shaped by geography and disease subtypes while encoding gene repertoires with the potential to influence host physiology, thereby providing a foundational resource for precision medicine.IMPORTANCEResearch on the human gut microbiome in IBS has focused primarily on bacteria, leaving the viral component as a vast and poorly understood reservoir. By profiling over 1,000 human samples globally, this study characterizes the taxonomic and functional features of the IBS gut virome. We demonstrate that these viral communities vary across geographic populations and IBS subtypes and are enriched in specific auxiliary metabolic genes, virulence factors, and antibiotic resistance genes. In addition, certain viral profiles show significant correlations with patient psychological symptoms such as anxiety and depression. This study also evaluates the potential of virome-based diagnostic biomarkers. Consequently, our findings provide a valuable reference for future in-depth research into the specific roles and mechanistic contributions of the gut virome in the pathogenesis of IBS.},
}

@article {pmid42861989,
year = {2026},
author = {Wang, G and Zhang, N and Peng, Y and Wen, X and Chen, X and Zou, M and Gao, S and Min, C and Min, X and Huang, J},
title = {Association of quantitative sputum Candida load with respiratory dysbiosis and airway inflammation in suspected invasive pulmonary candidiasis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0083726},
doi = {10.1128/msystems.00837-26},
pmid = {42861989},
issn = {2379-5077},
abstract = {UNLABELLED: The clinical significance of Candida species isolation from sputum remains ambiguous due to the colonization-infection dilemma. Integrating quantitative culture with microbiome profiling may clarify its role, yet systematic evidence is scarce. In this exploratory study (June 2023-June 2026), we enrolled 140 hospitalized patients suspected of invasive pulmonary candidiasis (IPC) and stratified them into possible IPC (n = 36), probable IPC (n = 71), and negative control (n = 33) groups based on clinical criteria. All underwent quantitative fungal culture of sputum and metagenomic next-generation sequencing (mNGS). Patients were stratified by sputum Candida species load into low (<10[5] CFU/mL), high (≥10[5] CFU/mL), and negative control (0 CFU/mL) groups. We investigated associations between Candida species burden, respiratory microbiota, local inflammation (IL-8), and clinical outcomes. Higher Candida species load was significantly associated with prolonged hospitalization, elevated sputum IL-8, an increased microbial dysbiosis index, and depletion of key commensals (e.g., Neisseria, Prevotella, Rothia, Streptococcus, and Veillonella). Counterintuitively, it correlated negatively with several classic bacterial pathogens (such as Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Pseudomonas aeruginosa). A random forest model identified a nine-species microbiome signature that effectively discriminated probable from possible IPC (AUC, 0.877; 95% CI, 0.662-0.944). In patients with suspected IPC, higher sputum Candida species load is associated with exacerbated respiratory dysbiosis and airway inflammation. Quantitative Candida species assessment combined with microbiome signatures may serve as a complementary tool for stratifying disease severity and ecological disruption, meriting further validation in larger, multicenter cohorts.

IMPORTANCE: Respiratory specimens dominate clinical fungal cultures, yet interpreting the role of Candida spp. in sputum remains a diagnostic dilemma. Here, by integrating quantitative culture with metagenomic sequencing, we show that a high sputum Candida species load is a marker of profound ecological disruption. High Candida species burden was associated with significant depletion of key commensals, an elevated dysbiosis index, and heightened local inflammation. Counterintuitively, it correlated negatively with several classic bacterial pathogens, revealing a distinct dysbiotic signature. Moreover, a microbiome-based model accurately discriminated patients with probable invasive pulmonary candidiasis. Our findings suggest that quantitative sputum Candida species load, interpreted within the context of the microbial community, may be a practical biomarker for identifying patients with significant respiratory dysbiosis and inflammation, offering a path toward more refined, ecology-informed therapeutic strategies.},
}

@article {pmid42862002,
year = {2026},
author = {Zhang, M and Ge, L and Liu, K and Liu, Y and Zhao, G and Kwok, LY and Sun, Z and Sun, Z and Zhang, W},
title = {Sex- and Time-Resolved Physiological and Gut Ecosystem Responses to a Food-Grade Microbiome-Targeted Intervention in Collegiate Endurance Athletes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77664},
doi = {10.1002/advs.77664},
pmid = {42862002},
issn = {2198-3844},
support = {NMGLLY2025-02//Inner Mongolia Autonomous Region Special Project for Scientific and Technological Innovation Research in Key Fields of the "Two Barriers," "Two Bases," and "One Bridgehead" Initiative/ ; 32325040//National Natural Science Foundation of China/ ; 32502149//National Natural Science Foundation of China/ ; U25A20733//National Natural Science Foundation of China/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {Endurance athletes experience sustained physiological demands during high-volume training, yet evidence for microbiome-targeted interventions in real-world settings remains limited. We conducted a two-stage, randomized, double-blind, placebo-controlled trial in 150 athletes allocated 2:1 to combined probiotics-yeast extract (CPYE) or placebo for 6 weeks; 44 completers confirmed for the 12th Inner Mongolia Autonomous Region University Games entered an exploratory 6-week extension with intensified training. Integrating wearable-derived phenotyping, field-based cardiorespiratory indices, clinical assessments, fecal metagenomics, and metabolomics, we found that during the randomized short-term phase, CPYE was associated with changes in device-estimated maximal oxygen uptake, exercise heart-rate indices, lactate, and redox biomarkers versus placebo. Exploratory sex-stratified analyses suggested heterogeneous response patterns, while the selected long-term extension indicated time-dependent changes requiring confirmation. Multi-omics identified sex- and phase-associated differences in microbial taxa, functions, metabolites, and network topology. Indirect-effect models nominated candidate features (rmlD, PISD-linked phosphatidylethanolamine pathways, Bacteroides ovatus, and folate-related functions) as potential indirect correlates of host outcomes. These findings support further evaluation of CPYE-associated responses in collegiate endurance athletes; subgroup, long-term, network, and indirect-effect results are hypothesis-generating.},
}

@article {pmid42854592,
year = {2026},
author = {Giannis, D and Gianni, P},
title = {Herpesvirus reactivation in critical illness: Pathogenesis, clinical consequences, and diagnostic challenges.},
journal = {Virology},
volume = {625},
number = {},
pages = {111097},
doi = {10.1016/j.virol.2026.111097},
pmid = {42854592},
issn = {1096-0341},
abstract = {Human herpesviruses (HHV) remain latent after primary infection and may reactivate during critical illness. HHV reactivation has been associated with adverse clinical outcomes, yet its pathogenic significance and optimal management remain unclear. This review summarizes the dysregulated immune mechanisms and risk factors for HHV reactivation in critical illness, treatment options, outcomes, current diagnostic challenges, and emerging precision medicine approaches. Critical illness induces profound immune dysregulation characterized by an initial hyperinflammatory response followed by immunosuppression, T-cell exhaustion, impaired natural killer cell function, and disrupted antiviral surveillance. These changes facilitate reactivation of latent HHV, including herpes simplex virus type 1 (HSV-1), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6). HSV and CMV reactivation in mechanically ventilated and septic patients have been associated with prolonged mechanical ventilation, longer intensive care unit (ICU) stay, secondary infections, and increased mortality. However, the distinction between clinically significant disease from asymptomatic reactivation remains challenging. Current evidence does not support routine antiviral prophylaxis in immunocompetent ICU patients. Emerging approaches including metagenomic next-generation sequencing, host transcriptomics, immune phenotyping, and multi-omics integration may improve risk stratification and identify patient subgroups that are most likely to benefit from targeted intervention. HHV reactivation may serve as a biomarker and potential mediator of adverse outcomes. Improved understanding of host-virus interactions, coupled with precision medicine that integrates virological and immunological data, is required to differentiate clinically relevant reactivation from epiphenomena and to guide individualized therapeutic strategies.},
}

@article {pmid42854651,
year = {2026},
author = {Molendijk, MM and Prasad, DK and Worp, N and Schapendonk, CME and Nieuwenhuijse, D and Aarestrup, FM and Verbon, A and van Wamel, WJB and Koopmans, MPG and de Graaf, M},
title = {Metagenomic insights into the global occurrence of ESKAPE-targeting bacteriophages in urban wastewater.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127032},
doi = {10.1016/j.watres.2026.127032},
pmid = {42854651},
issn = {1879-2448},
abstract = {Antimicrobial resistance (AMR) poses a serious threat to global public health, with Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species - collectively known as ESKAPE pathogens - as high priority threats. Bacteriophages represent a potential alternative therapy for AMR infections. While many of the bacteriophages that target ESKAPE pathogens have been isolated from environmental sources, such as wastewater, the global distribution of these bacteriophages remains poorly understood. In this study, metagenomic sequencing of wastewater was used to assess the presence and distribution of known bacteriophages in urban wastewater collected from 62 sites worldwide. Focusing specifically on lytic bacteriophages known to target ESKAPE pathogens, a literature review was conducted to curate a collection of bacteriophages with known therapeutic properties and publicly available genomes. The presence and distribution of these therapeutic bacteriophages in wastewater were examined, both geographically and temporally. Our analysis revealed a high abundance of bacteriophage families associated with the human gastrointestinal tract, as well as those infecting bacteria native to aquatic environments. Bacteriophages similar to those targeting ESKAPE pathogens were detected across the wastewater samples, except for bacteriophages targeting Staphylococcus aureus. Both the presence and abundance of these putative ESKAPE-phages varied considerably across regions, with African sample sites exhibiting the highest diversity and European sample sites the lowest. No clear temporal trends were observed for these bacteriophages. This study provides the use of wastewater to provide insights into the global diversity and distribution of bacteriophages, with a specific focus on species with therapeutic potential against ESKAPE pathogens, while further offering a valuable dataset for future bacteriophage research.},
}

@article {pmid42854696,
year = {2026},
author = {Cabello-Yeves, E and Samarra, A and Summers, K and Comas, I and Wellington, E and Millard, A and Collado, MC and Marina, A},
title = {Breastfeeding and maternal microbial reservoirs are associated with infant gut phageome development during the first year of life.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103107},
doi = {10.1016/j.xcrm.2026.103107},
pmid = {42854696},
issn = {2666-3791},
abstract = {The early-life assembly of the gut microbiome is a critical determinant of long-term health, yet the role of bacteriophages in this process remains poorly understood. Here we longitudinally profile the gut phageome of 34 mother-infant dyads during the first year of life with metagenomics and a phage-centered computational workflow. Phage diversity increases with age, paralleling bacterial diversification but following distinct ecological trajectories. Shared viral populations across maternal and infant samples are consistent with potential maternal contribution, although not indicative of direct transmission. Feeding-related variables are consistently associated with phageome composition at specific developmental stages. No single factor fully explains phageome variation, supporting a multifactorial model involving maternal, environmental, and dietary inputs. Together, these findings provide a framework for understanding early-life phage ecology, positioning phages as active participants in early microbiome assembly and supporting the inclusion of viral components in microbiome-based strategies aimed at promoting healthy ecosystem development in infancy.},
}

@article {pmid42854797,
year = {2026},
author = {Huang, Y and Yang, S and Wei, P and Zhou, H and Zhang, F and Li, X and Zhang, S},
title = {Ca/Fe-modified drinking water treatment residue with Vallisneria natans controls algal blooms via phosphorus transformation and smicrobial network shifts.},
journal = {Bioresource technology},
volume = {464},
number = {Pt C},
pages = {136025},
doi = {10.1016/j.biortech.2026.136025},
pmid = {42854797},
issn = {1873-2976},
abstract = {Internal phosphorus (P) loading is a key driver of algal blooms in shallow lakes, yet submerged macrophyte (SM) restoration alone often fails because clear water also favors epiphytic filamentous algae and regime shifts. We constructed a co-remediation system combining Ca/Fe-modified drinking water treatment residue (Ca/Fe-DWTR) with Vallisneria natans and ran a 183-day microcosm experiment to reveal how sediment P transformation coupled with macrophyte restoration controls water quality and suppresses two different algal blooms. Co-remediation markedly reduced sediment total-P and mobile-P while increasing stable-P forms, and no bloom occurred throughout cultivation, with chlorophyll a below 1.5 μg/L. The nitrogen (N) release risk associated with Ca/Fe-DWTR alone was also eliminated. Conversely, unremediated-sediment sustained planktonic blooms through sulfide-driven Fe bound P release coupled with nitrogen fixation, whereas the SM-only treatment stayed clear early but later developed massive epiphytic filamentous algae once photosynthetic pH rise mobilized Al bound P, confirming that success depends on P-stabilization rather than transient clarity. Metagenomics showed that co-remediation created low-P and oxidative niches that restructured microbial communities, enhancing nitrogen cycling potential in the phyllosphere while suppressing sulfate-reducing bacteria in sediment, thereby achieving coupled N and P removal within a resilient functional gene network. Mantel tests and PLS-SEM revealed that pH elevation by V. natans enhanced microbial P fixation and stable-P formation, while Ca/Fe-DWTR most strongly drove nitrogen transformation, and thus sediment P transformation indirectly governed water quality through microbial functional gene networks. Overall, the co-remediation showed potential for mitigating internal P loading and algal proliferation in shallow eutrophic lakes.},
}

@article {pmid42854799,
year = {2026},
author = {Wei, D and Zhai, FS and Zhao, CF and Zhang, YF and Wei, Q and Ni, SQ},
title = {Dissolved organic nitrogen molecular transformation and microbial mechanisms in a completely autotrophic nitrogen removal over nitrite (CANON)-based algal-bacterial symbiotic system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136037},
doi = {10.1016/j.biortech.2026.136037},
pmid = {42854799},
issn = {1873-2976},
abstract = {Sunlight-driven CANON-based algal-bacterial symbiotic system (CANON-AB) achieves efficient nitrogen removal through algal oxygen production and assimilation. However, dissolved organic nitrogen (DON), as a major fraction of residual total dissolved nitrogen, remains poorly understood in CANON-AB. This study investigated DON transformation and microbial mechanisms in CANON-AB compared with conventional CANON. After 140 days operation, CANON-AB increased average dissolved inorganic nitrogen (DIN) removal efficiency from 83.6 % to 98 %, reducing effluent nitrate from 27.4 ± 8.3 to 0.7 ± 0.8 mg/L. Meanwhile, DON concentration decreased by 54.8 % in CANON-AB (1.4 ± 0.2 mg/L) compared with CANON (3.1 ± 0.2 mg/L). FT-ICR MS revealed that algae integration reduced DON molecular diversity from 1396 to 723 formulas, with preferential removal of carbohydrates, condensed aromatics, tannins, and sulfur-containing DON molecules. Metagenomic analysis demonstrated enhanced DON mineralization potential in CANON-AB, with DON transformation genes enriched by 1.1-2.4 times higher compared with CANON. These results reveal a coupled mineralization-assimilation mechanism driving DON removal in CANON-AB, providing new insights into nitrogen cycling in sustainable wastewater treatment.},
}

@article {pmid42854800,
year = {2026},
author = {Peng, Y and Yu, H and Sun, F and Huang, X and Wei, L and Chen, C},
title = {Molecular transformation of dissolved organic matter during landfill leachate treatment by microbial electrolysis cell-anaerobic digestion system.},
journal = {Bioresource technology},
volume = {464},
number = {Pt C},
pages = {136038},
doi = {10.1016/j.biortech.2026.136038},
pmid = {42854800},
issn = {1873-2976},
abstract = {The complex dissolved organic matter (DOM) in landfill leachate posed significant challenges for conventional biological treatment. In this study, a microbial electrolysis cell-anaerobic digestion (MEC-AD) system was constructed to explore DOM transformation pathways. An orthogonal experimental design was employed to evaluate the effects of applied voltage, anode-to-cathode area ratio, and stainless-steel cathode mesh size. Under an applied voltage of 1.2 V, an anode-to-cathode area ratio of 1:1, and a cathode mesh size of 200 mesh, the highest overall COD removal efficiency of 60.2% was observed. Spectroscopic analysis showed a reduction in biodegradable soluble microbial byproducts during treatment. GC-MS showed changes in the profiles of representative aliphatic and aromatic compounds. FT-ICR MS analysis revealed compositional reorganization of DOM, characterized by the disappearance of a fraction of protein- and lipid-like DOM and the persistence or relative enrichment of more unsaturated and aromatic constituents. Microbial community analysis revealed the relative enrichment of hydrolytic and fermentative bacteria (e.g., norank_f__Anaerolineaceae) as well as bacteria potentially involved in electron transfer (e.g., Thiobacillus). Metagenomic analysis suggested functional potential for amino acid metabolism, fatty acid degradation, glycolysis, and pyruvate metabolism. In contrast, the relatively low abundance of aromatic compound degradation functions was consistent with the persistence of refractory aromatic DOM. This study revealed that MEC-AD treatment was associated with differential transformation and molecular reorganization of landfill leachate DOM, and provided molecular-level insights beyond conventional bulk organic matter removal.},
}

@article {pmid42854825,
year = {2026},
author = {Zhang, Y and Lu, R},
title = {Characteristics of metagenome and metabolomics of biliary flora in biliary acute pancreatitis for severity prediction.},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {102625},
doi = {10.1016/j.gassur.2026.102625},
pmid = {42854825},
issn = {1873-4626},
abstract = {OBJECTIVE: To investigate the characteristics of the metagenome and metabolomics of biliary flora in patients with acute biliary pancreatitis and its predictive value for the severity of the disease.

METHODS: This study included 80 ABP patients (Jan 2022 - Dec 2024) and 30 healthy controls. ABP patients were divided into mild (n = 50) and moderate-severe (n = 30) groups using the revised Atlanta criteria. Chao1 index, Shannon index, relative abundances of Klebsiella, Enterococcus, and Escherichia coli, serum amylase, and C-reactive protein (CRP) were compared. ROC analysis assessed predictive value of Shannon index, Klebsiella abundance, and CRP for severity. Correlations between these parameters and severity were examined.

RESULTS: Significant differences were observed among the three groups in Chao1 and Shannon indices, relative abundances of the three bacterial genera, and serum amylase and CRP levels (all P < 0.05). ROC analysis showed that Shannon index, Klebsiella relative abundance, and CRP level predicted disease severity with AUCs of 0.804, 0.804, and 0.850, respectively (P < 0.05). Shannon index was negatively correlated with ABP severity, while Klebsiella abundance and CRP level were positively correlated with severity (P < 0.05).

CONCLUSION: In this cohort, biliary microbiome characteristics and serum inflammatory markers were associated with the severity of biliary acute pancreatitis. The Shannon index, Klebsiella relative abundance, and CRP showed exploratory discriminatory performance. These findings provide a basis for further prospective validation; they do not establish a causal driving factor, a clinically validated early-warning system, or an individualized treatment strategy.},
}

@article {pmid42854947,
year = {2026},
author = {Yang, Y and Yu, H and Wang, J and Yang, S and Han, J and Jin, W and Luo, D and Zhou, S and Ma, C},
title = {Species-associated toxicological trajectories in social bees exposed to sublethal metribuzin: A multi-omics perspective on host-microbiome interactions.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {411},
number = {Pt A},
pages = {129320},
doi = {10.1016/j.envpol.2026.129320},
pmid = {42854947},
issn = {1873-6424},
abstract = {The divergent sensitivities of honeybees (Apis mellifera) and bumblebees (Bombus terrestris) to agrochemicals challenge the one-species-fits-all framework of ecological risk assessment, yet the mechanistic basis for this variation remains underexplored. Here, we used an integrated multi-omic approach, combining transcriptomics, metabolomics, and gut metagenomics, to map the species-associated responses of these pollinators under sublethal metribuzin (MET) exposure (30 mg/kg). Honeybees, exhibited broad transcriptional activation accompanied by suppressed P450 and glutathione S-transferase (GST) activities, metabolically associated with a disruption in cellular cofactor (NADPH/FAD) biosynthesis pathways, coincided with midgut tissue pathology and microbial structural dysbiosis. Conversely, bumblebees showed targeted cytochrome P450 (CYP) induction and elevated P450/GST activities, linked to an energy-intensive rewiring of carbohydrate metabolism that supported both xenobiotic clearance and antioxidant defense. While the bumblebee gut microbiota remained structurally stable, it displayed functional shifts toward xenobiotic efflux and cellular cytoprotection. Collectively, our multi-omic landscapes delineate two divergent correlative models: metabolic impairment coupled with microbial dysbiosis in honeybees, versus physiological resilience associated with microbiome functional plasticity in bumblebees. These findings propose a testable framework wherein baseline metabolic capacity shapes species-associated trajectories of host-microbiome interactions under herbicide stress, highlighting the critical need to incorporate mechanistic insights from multi-species comparisons into future ecological risk assessments.},
}

@article {pmid42856459,
year = {2026},
author = {Takeuchi, T and Reddy, A and Robinson, EK and Kotaka, KM and Higginbottom, SK and Sonnenburg, ED and Sonnenburg, JL},
title = {Functional Divergence in Gut Clostridia from Hadza Hunter-Gatherers Reveals Diet-Adapted Metabolic Machinery That Shapes Gut Ecology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.29.755216},
pmid = {42856459},
issn = {2692-8205},
abstract = {Lifestyle changes associated with industrialization, including shifts in diet, are linked to extensive remodeling of the human gut microbiome. Investigating the gut microbiomes of traditional populations living non-industrialized lifestyles, such as the Hadza hunter-gatherers of Tanzania, therefore offers insight into bacterial taxa and functions depleted in industrialized microbiomes. Despite pronounced compositional differences that correspond to lifestyle, many commensal gut species are shared between industrialized and non-industrialized populations, raising a fundamental question of whether and how their functional repertoires diverge across contrasting gut environments. Here, by integrating strain-resolved metagenomics with culturomics and in vivo models, we identify phylogenetic and functional divergence within prevalent gut species shared between Hadza and industrialized populations, particularly among members of the Clostridia class. Dorea longicatena , prevalent across diverse human populations independent of lifestyle, is a poorly characterized member of Clostridia. Using strains of this D. longicatena isolated from either Hadza or industrialized human stool samples, we uncover metabolic pathways selectively enriched in Hadza strains, including machinery for utilizing plant-derived pectic polysaccharides. We further demonstrate that this Hadza-enriched polysaccharide-utilization machinery can be leveraged with its cognate dietary substrate to promote D. longicatena colonization within a model industrialized microbiota, reshaping intestinal and portal-vein metabolite profiles. Together, our findings reveal substantial functional divergence within gut bacterial species shared across lifestyles, providing a framework for identifying diet-responsive strains and pathways that may complement ecological and metabolic functions underrepresented in industrialized microbiotas.},
}

@article {pmid42856497,
year = {2026},
author = {Tisza, MJ and Simar, SR and Zorz, JK and Javornik Cregeen, SJ and Maresso, AW},
title = {EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.29.755457},
pmid = {42856497},
issn = {2692-8205},
abstract = {Metagenomic sequencing allows for detection of any number of pathogenic viruses from a single sample without a priori knowledge of its contents. This has created a substantial opportunity to characterize pathogens in humans and their environment, but the field is held back by a lack of bioinformatics tools for taxonomic profiling and reconstructing virus genomes. The ideal profiler would simultaneously do two things: report viruses at single-read sensitivity so that ultra-low-abundance pathogens are not missed and hold near-perfect specificity so that a pathogen is never falsely reported. Here we present EsViritu , a taxonomic profiler that pairs an iterative greedy clustering algorithm and lowest-common-ancestor taxonomic refinement with a curated Virus Pathogen Database to reconstruct virus genomes and generate virome profiles directly from reads. We benchmarked EsViritu against four leading metagenomic profilers (Kraken2, Centrifuger, Metabuli , and Sylph), running each program across a full parameter sweep and against the same Virus Pathogen Database for an apples-to-apples comparison. Across synthetic positive controls, pathogen-free negative controls, and mutated mock communities, EsViritu was the most accurate tool at reconstructing community composition: it led or tied every tool on relative abundance accuracy at all taxonomic ranks and led or tied on detection across ranks. Importantly, other tools frequently report the presence of multiple related taxa when only reads for a single genome are present, but EsViritu faithfully records the correct, single taxon and genome. EsViritu achieves read-level sensitivity for sequences as low as 85% average nucleotide identity to the nearest reference and reports essentially no false positives in pathogen-free host and synthetic samples. EsViritu also returns reconstructed consensus genomes whose nucleotide identity to the nearest reference closely tracks ground truth, yielding both a profile and genomes from a single run.},
}

@article {pmid42856507,
year = {2026},
author = {Din, MO and Brennan, C and Zhao, J and Oles, R and Patel, L and Birmingham, A and Sevilir, DM and Hansen, L and Wright, GM and Ambre, M and Tomita, M and Boyer, T and Gonzalez, A and Ackermann, G and McDonald, D and Kralicek, S and Hecht, G and Hasty, J and Smarr, L and Knight, R},
title = {Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.28.754546},
pmid = {42856507},
issn = {2692-8205},
abstract = {Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.},
}

@article {pmid42856590,
year = {2026},
author = {Zhang, J and Zhang, L and Li, SG and Li, J and Zou, Y and Long, T and Yu, R and Zhang, Y},
title = {Case Report: Sequencing-supported probable osteoarticular Mycobacterium avium complex infection in rheumatoid arthritis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1954797},
pmid = {42856590},
issn = {2296-858X},
abstract = {BACKGROUND: Osteoarticular Mycobacterium avium complex (MAC) infection is uncommon and can resemble inflammatory arthritis during immunosuppression.

CASE DESCRIPTION: A 52-year-old woman with an erosive seronegative rheumatoid arthritis phenotype and overlap autoimmune features developed progressive polyarticular swelling, wrist tenosynovitis, hip effusions, and low-back pain after cumulative immunosuppression. Investigations showed macrocytic anemia, lymphopenia, pan-hypogammaglobulinemia, marked B-cell depletion without anti-CD20 exposure, and cytomegalovirus DNAemia. Pre-treatment mNGS reported MAC-spectrum signals in hip, wrist, and elbow aspirates, including 355 right-hip reads. A separate pathogen-targeted joint-fluid sequencing report, with no anatomical site stated, detected MAC complex (116,330 normalized sequences; assay-estimated 10⁵ copies/mL). Neither result was interpreted as organism burden. No tissue histopathology, dedicated mycobacterial culture, or phenotypic susceptibility testing was performed. The working diagnosis was multisite sequencing-supported probable multifocal osteoarticular MAC infection without culture confirmation. Several interventions began concurrently. Selected follow-up MR images showed persistent destructive wrist disease and residual joint or periarticular fluid, but no standardized imaging or microbiological response endpoint was available.

CONCLUSION: In atypical arthritis progressing during immunosuppression, infection-focused sampling should precede further escalation. mNGS can provide an etiologic clue, but culture, histopathology, targeted testing, and longitudinal reassessment remain essential.},
}

@article {pmid42856639,
year = {2026},
author = {Strength, RE and Angelova, A and Robbins, E and Levy, S and McCauley, KE and Lloyd, KM and Margolis, EB and Burns, AS and Mistry, S and Subramanian, P and Dassner, A and Zerbe, C and Band, VI and Namasivayam, S and Chen, Q and Esadah, E and Rees, K and Bacorn, M and Prasad, R and LaPoint, P and Romero-Soto, HN and Dekker, JP and Sears, CL and Shapiro, C and Hamdy, RF and Campos, JM and Hourigan, SK},
title = {Coming Into Resistance: Clinically Important Antibiotic Resistance Genes in NICU vs. Healthy Infants.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.26363796},
pmid = {42856639},
abstract = {IMPORTANCE: Antibiotic-resistant infections in neonates often arise from the infant's own colonizing bacteria harboring antibiotic resistance genes (ARG). This study evaluates ARG that impact antibiotic selection and drive resistance-related mortality, termed clinically important antibiotic resistance genes (CI-ARG).

OBJECTIVE: To determine differences in gut CI-ARG abundance in children from birth through 3 years old, stratified by neonatal intensive care unit (NICU) admission and antibiotic (abx) exposure in the first two months.

DESIGN: Cohort study (sequencing, analysis completed 2025-2026) using shotgun metagenomic sequencing of stool samples from infants in two studies: "Neonatal Intestinal Microbiome" (+NICU groups, 2015-2022), "The First 1000 Days of Life and Beyond" (-NICU groups, 2018-2021). Infants grouped into four cohorts: +NICU/+abx, +NICU/-abx, -NICU/-abx, and -NICU/+abx. Prespecified CI-ARG abundance compared longitudinally among groups.

SETTING: NICU, well-baby nursery, Inova Fairfax Hospital, Virginia.

PARTICIPANTS: +NICU criteria: admission to the NICU, anticipated length of stay (LOS) of at least five days, maternal age ≥18 years. -NICU: parents with good general health and age ≥18 years enrolled prior to infant birth. Stool samples: adequate stool processing volume, at least one stool sample from before one month and after one year of age, 7-day minimum between serial samples.

EXPOSURES: NICU versus well-baby nursery; antibiotics versus none in first two months of corrected age.

MAIN OUTCOMES AND MEASURES: Predefined primary outcome-longitudinal CI-ARG abundance by group, compared using linear mixed effects models with adjustment for multiple comparisons (Benjamini-Hochberg procedure). Predefined secondary outcomes-differences in overall microbiota and resistome composition.

RESULTS: 1000 serial stool samples, 179 infants (birth-39 months). Longitudinal abundance significantly differed among cohorts for 11 CI-ARG (p<0.05); often higher in the +NICU groups in early life, with or without antibiotic exposure. Abundance of ARG conferring resistance to aminoglycosides, macrolides, and fluoroquinolones later decreased below -NICU levels. mecA , which often drives methicillin resistance in Staphylococcus , was detected only in +NICU infants during premature period.

CONCLUSIONS: This longitudinal study demonstrates significant longitudinal CI-ARG differences in children grouped by early-life NICU status and/or antibiotic exposure. Future studies should explore the mechanisms driving these CI-ARG changes and evaluate their impact on infection risk and community spread.

KEY POINTS: Question: How do clinically important antibiotic resistance genes (CI-ARG) differ longitudinally among infants up to 3 years old based on NICU admission and antibiotic exposure in the first two months of life?Findings: In this cohort study of 179 infants through 39 months of age, longitudinal abundance was significantly different for 11 prespecified CI-ARG, often higher in the NICU groups in early life, with or without antibiotic exposure.Meaning: Children with a history of NICU hospitalization, whether due to the NICU environment itself, prematurity, or other factors, may have increased CI-ARG burden early in life, irrespective of direct antibiotic exposure.},
}

@article {pmid42856694,
year = {2026},
author = {Soveral, LF and Holanda, LRL and Assunção, IBF and Gomes, LG and de Souza, IB and Rodrigues, GS and Vanny, PA and Bruna-Romero, O and Palmeiro, JK and Scheffer, MC and Sincero, TCM and Zárate-Bladés, CR},
title = {Identification of antibiotic resistance genes in fecal microbiota selected donors during the establishment of a biobank in the south of Brazil.},
journal = {Frontiers in antibiotics},
volume = {5},
number = {},
pages = {1905540},
pmid = {42856694},
issn = {2813-2467},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is increasingly explored for other dysbiosis-related disorders. However, its implementation as a regulated therapeutic strategy requires robust donor screening, biosafety frameworks, and standardized processing workflows. Here, we describe the establishment of the first fecal microbiota biobank in southern Brazil and evaluate the incorporation of metagenomic sequencing as a complementary layer of donor characterization and safety assessment. A structured donor selection pipeline based on international guidelines was implemented, integrating clinical screening, biochemical and serological testing, and microbiological analyses. Of 100 screened candidates, only four donors met all eligibility criteria and were included in the biobank, highlighting the stringency of the selection process. Shotgun metagenomic sequencing revealed a diverse resistome across all donors, including a shared core set of resistance genes alongside marked interindividual variability. Dominant resistance determinants included tetracycline-associated genes, ermF, CfxA-type β-lactamases, and aminoglycoside-modifying enzymes, which were associated with specific gut taxa. Genomic context analysis further identified four ARG-containing contigs with features compatible with potential mobility, although active horizontal gene transfer was beyond the scope of this study. Notably, tet(Q) and ermF were predominantly associated with Bacteroides fragilis, supporting its role as a reservoir of resistance determinants in the gut microbiota. These findings support the use of metagenomic profiling as a complementary approach to donor characterization and risk assessment rather than as a standalone criterion for donor exclusion. Overall, this study provides a framework for microbiota biobank implementation and highlights the potential of metagenomic analysis to complement conventional biosafety screening in FMT.},
}

@article {pmid42856732,
year = {2026},
author = {Wallace, BA and Baker, L and Papke, E and Ushijima, B and Rosales, SM and Silveira, CB},
title = {Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease.},
journal = {Coral reefs (Online)},
volume = {45},
number = {5},
pages = {2211-2230},
pmid = {42856732},
issn = {1432-0975},
abstract = {UNLABELLED: Lysogenic conversion, in which bacteriophages (viruses that infect bacteria) integrate into bacterial genomes and confer new phenotypic traits on their hosts, is a well-established mechanism for the emergence of pathogens. While this process underpins many bacterial diseases in humans and other animals, its role in coral disease remains largely unexplored. Here, we investigate the potential role of lysogenic conversion in stony coral tissue loss disease (SCTLD), which has caused unprecedented mortality of Caribbean corals since 2014 and for which the etiological agent remains unknown. Across 27 original coral samples and 174 publicly available metagenomes from the Florida Reef Tract spanning seven coral species, we detected a greater number of unique viral genomes harboring genomic features associated with lysogeny in diseased corals or visually healthy portions of diseased corals (DD and HD, respectively) compared to visually healthy (VH) corals. SCTLD-associated bacteriophages were primarily predicted to infect bacterial taxa previously implicated in the disease, such as Vibrionales, Rhodobacterales, and Flavobacteriia, and carried abundant and widespread virulence factors with the potential to enhance bacterial colonization, competition, or direct host damage, including homologs of Tse2, Zot, RTX, pneumolysin, and cytolytic delta-endotoxin. Although causal relationships remain unresolved, our findings indicate that phages have the genomic capacity to laterally transfer bacterial virulence genes in SCTLD-affected corals. The acquisition of genes via lysogenic conversion could contribute to bacterial virulence while maintaining community taxonomic profiles, helping to explain previous community profiling observations and providing a mechanistic framework for disease pathogenesis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s00338-026-02902-2.},
}

@article {pmid42856881,
year = {2026},
author = {Ding, L and Wang, H and Li, F},
title = {Case Report: Streptococcus suis-associated meningoencephalitis with profound bilateral labyrinthine deafness and intra-operative cochlear fibrosis treated by cochlear implantation.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1941314},
pmid = {42856881},
issn = {2296-858X},
abstract = {Streptococcus suis is a common zoonotic pathogen that usually causes monomicrobial meningitis. Occult bloodstream detection of Klebsiella pneumoniae, together with proven central-nervous-system S. suis infection, followed by irreversible cochlear fibrotic changes requiring cochlear implantation, appears exceptionally rare. We report a 52-year-old male with chronic heavy alcohol intake and occupational swine-exposure history who developed severe sepsis, recurrent suppurative meningoencephalitis caused by S. suis, and permanent bilateral labyrinthine-related deafness. Combined blood and cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) identified suspected additional bloodstream infection by K. pneumoniae, although K. pneumoniae was not detected in CSF. Multimodal antimicrobial, anti-inflammatory, and immunomodulatory therapy cleared intracranial infection but failed to restore hearing. Preoperative imaging suggested cochlear fibrotic changes; left-sided cochlear implantation achieved full electrode insertion with stable intraoperative neural responses despite abundant intracochlear fibrous tissue observed intraoperatively. This case raises three important considerations: occupational swine exposure together with chronic alcoholism may plausibly contribute to suspected polymicrobial sepsis; in selected patients, peripheral-blood mNGS may help identify occult Gram-negative bacteremia when CSF assays remain negative during recurrent meningitis; and cochlear fibrosis may not absolutely preclude technically-successful cochlear implantation.},
}

@article {pmid42857043,
year = {2026},
author = {Fang, C and Wang, C and Wang, R and Lu, YF and Ma, L},
title = {Gut microbial characteristics and kynurenine-related metabolism across sarcopenia groups: associations with neuromuscular and physical function.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1883616},
pmid = {42857043},
issn = {1663-4365},
abstract = {BACKGROUND: Sarcopenia is characterized by heterogeneous alterations in muscle mass, strength, and physical performance and may involve interactions among the gut microbiota, tryptophan metabolism, and neuromuscular function. However, these biological characteristics across different sarcopenia stages remain incompletely understood. This study investigated gut microbial characteristics, kynurenine-related metabolism, circulating biomarkers, and physical function in older adults with different sarcopenia status.

METHODS: In this cross-sectional study, 67 older adults were classified according to the Asian Working Group for Sarcopenia 2019 criteria as non-sarcopenia (NSG, n = 17), possible sarcopenia (PSG, n = 20), or sarcopenia (SG, n = 30). Muscle mass, handgrip strength, and multidimensional physical performance were assessed. Serum C-terminal agrin fragment (CAF), tumor necrosis factor-α (TNF-α), amino acids, kynurenine (KYN), and tryptophan (Trp) were measured, and the KYN/Trp ratio was calculated. Gut microbiome composition was characterized by shotgun metagenomic sequencing. Differential abundance was evaluated using MaAsLin2 with adjustment for age and body mass index (BMI), and exploratory correlations among microbial genera, metabolites, circulating biomarkers, and physical function were examined with false discovery rate correction.

RESULTS: ASMI was significantly lower in the SG group than in the NSG and PSG groups, whereas several measures of physical performance differed among groups without a uniform stepwise pattern. No significant differences were observed in alpha diversity, beta diversity, or the Firmicutes/Bacteroidetes ratio, and sarcopenia group explained only 3% of the variation in overall microbial community composition (PERMANOVA, R [2] = 0.03, p = 0.226). Several genus-level associations were nominally significant after adjustment for age and BMI, but none remained significant after BH-FDR correction. After adjustment for age and BMI, serum KYN concentrations and the KYN/Trp ratio were significantly higher in the SG group than in the NSG group (p = 0.011 and p = 0.043, respectively), whereas Trp and the measured amino acids showed no significant pairwise differences. The unadjusted increase in CAF across sarcopenia groups was attenuated after covariate adjustment, and TNF-α did not differ significantly among groups. Exploratory correlation analyses identified several FDR-significant associations across microbial, metabolic, and functional domains, including negative associations of KYN and KYN/Trp with handgrip strength and a positive association between CAF and 6-m gait speed(GS).

CONCLUSION: Established sarcopenia was associated with altered circulating kynurenine-related metabolism despite the absence of pronounced differences in overall gut microbial community structure. Exploratory cross-domain associations further suggest potential interactions among gut microbial characteristics, tryptophan metabolism, and neuromuscular and physical function. These findings support further investigation of host-microbial tryptophan metabolism in sarcopenia but do not establish a causal microbiota-kynurenine-NMJ pathway.},
}

@article {pmid42857110,
year = {2026},
author = {Zou, X and Chen, Q and Pu, W and Gao, J and Yang, Y and Long, X},
title = {Dietary American Cockroach (Periplaneta americana) Chitin Influences Growth Performance, Nutrient Utilization, Gut Microbiota, and Riboflavin-Related Metabolism in Juvenile Grass Carp (Ctenopharyngodon idella).},
journal = {Aquaculture nutrition},
volume = {2026},
number = {},
pages = {3097646},
pmid = {42857110},
issn = {1365-2095},
abstract = {The American cockroach (Periplaneta americana) is an emerging sustainable source of insect-based chitin, yet its physiological effects and optimal inclusion levels in herbivorous fish diets remain undefined. This study evaluated the dose-dependent effects of dietary P. americana chitin (0%, 2.5%, 5%, 10%, and 20%) on juvenile grass carp (Ctenopharyngodon idella) over a 63-day trial. Results revealed a distinct biphasic response in growth and nutrient utilization. Fish fed the 5% chitin diet exhibited the highest weight gain and specific growth rate (SGR), coinciding with the highest apparent digestibility coefficient (ADC) of crude protein (74.34%) compared with the control (72.01%). Conversely, higher inclusion levels (10% and 20%) significantly suppressed growth and reduced protein digestibility. Metagenomic reanalysis showed that the riboflavin-biosynthesis gene ribA (K01497) was significantly reduced at 2.5%-10% dietary chitin (F (4,10) = 7.78, FDR p = 0.041), while the overall riboflavin metabolism pathway, the M00125 biosynthesis module, and intestinal riboflavin levels did not differ significantly among diets. Among the inclusion levels tested, 5% produced the most favorable overall response under the present experimental conditions, balancing improved growth and protein digestibility with the negative responses observed at higher inclusion levels.},
}

@article {pmid42857159,
year = {2026},
author = {Galetović, A and Ortiz, J and Peña, G and Arros, P and Guerra-Leal, N and Berríos-Pastén, C and Silva, M and Acosta, J and Varas, MA and Allende, ML and Marcoleta, AE},
title = {A genome-resolved cyanobacterial consortium from the Atacama Desert reveals novel bacterial diversity, stress-resilience potential, chromatic flexibility, and photoprotection.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1939861},
pmid = {42857159},
issn = {2296-4185},
abstract = {The Atacama Desert is one of the most extreme terrestrial environments on Earth, characterized by hyper-aridity, intense solar and ultraviolet radiation, oxidative stress, and metal-rich substrates. Here, we characterized an enriched cyanobacteria-associated consortium obtained from a high-altitude, river-influenced site in Quebrada Talabre, Atacama Desert. Deep shotgun metagenomic sequencing, achieving 99.7% estimated community coverage, enabled the reconstruction of 14 high-quality metagenome-assembled genomes representing five bacterial phyla. Genome-resolved analyses revealed multiple putative novel bacterial lineages, including a potential novel family-level lineage within Thermomicrobiales, putative novel species of Allosphingosinicella, Flavobacterium, and Caulobacter, and a distinct Nostocaceae lineage corresponding to the dominant cyanobacterium, tentatively named Talabrenema galetoviciae TAL-12. Functional annotation revealed marked differentiation among consortium members. Heterotrophic bacteria encoded predicted functions associated with aromatic compound degradation, nitrogen and sulfur turnover, iron acquisition, metal-biocide resistance, and oxidative-stress responses, whereas the TAL-12 cyanobacterial metagenome-assembled genome encoded the core machinery for oxygenic photosynthesis, carbon fixation, and pigment biosynthesis. Phylogenomic analyses supported T. galetoviciae TAL-12 as a novel species and likely novel genus within Nostocaceae. Comparative genomic and structural analyses revealed a diversified phycobiliprotein repertoire comprising phycocyanin, allophycocyanin, and phycoerythrocyanin components, together with divergent but structurally conserved paralogs and variable accessory pigment modules across related Nostocaceae genomes, consistent with enhanced light-harvesting flexibility. Pigment fractionation supported the absence of canonical phycoerythrin production and confirmed phycocyanin enrichment. Purified TAL-12 phycocyanin displayed moderate thermal stability, while the cyanobacterial component of TAL-12 consortium cultures retained chlorophyll during prolonged exposure to elevated temperature. In addition, the TAL-12 cyanobacterial genome encoded a Nostocales-like scytonemin biosynthetic gene cluster consistent with UV photoprotection, while lacking canonical cyanotoxin biosynthetic gene clusters. Together, these findings reveal previously underexplored bacterial diversity and predicted functional complementarity within an Atacama cyanobacteria-associated consortium, while identifying T. galetoviciae TAL-12 as a distinctive Nostocaceae lineage with light-harvesting, thermal-resilience, and photoprotective traits relevant to extremophile-based bioinnovation.},
}

@article {pmid42857378,
year = {2026},
author = {Zhang, Y and Cidan, Y and Xu, J and Li, B},
title = {CRC-TrustBench: benchmarking cross-study and cross-country generalization in gut metagenomic colorectal cancer prediction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1971707},
pmid = {42857378},
issn = {1664-302X},
abstract = {BACKGROUND: Gut metagenomic classifiers for colorectal cancer (CRC) are often evaluated with random splits that place samples from the same studies, countries, or processing workflows in both training and test sets, potentially inflating apparent performance. We developed CRC-TrustBench, a leakage-aware framework for evaluating cross-study and cross-country generalization and probability reliability.

METHODS: From 2,340 MetaGenoPolis V16 source samples, we curated 1,953 CRC or healthy samples from 15 studies and 10 countries; 185 adenoma samples were retained outside binary model development as a challenge population. Subject-aware random, leave-one-study-out (LOSO), and leave-one-country-out (LOCO) protocols were applied to taxonomic profiles with 2,543 features and functional profiles with 378 features. We compared Elastic Net, LightGBM, cohort-balanced Elastic Net, and pre-specified neural domain-robust methods using fold-specific pre-processing. The Microbiome Leakage and Confounding Audit (MiLCA) quantified study and country shortcuts, while Platt calibration, conformal-style sets, and selective abstention were evaluated without outer-test labels.

RESULTS: For taxonomic profiles, LightGBM achieved an area under the receiver operating characteristic curve (AUROC) of 0.874 under random splitting, 0.827 under LOSO, and 0.821 under LOCO; the single pre-specified RANDOM estimate was numerically higher than the held-out-domain summaries. Microbiome profiles predicted study and country identity, and a descriptive feature-level audit indicated pervasive study-associated structure. Cohort balancing yielded limited gains, and neural domain-robust methods did not consistently outperform LightGBM. Platt scaling reduced the mean LOCO Brier score from 0.180 to 0.169 and log loss from 0.630 to 0.521. LightGBM conformal-style coverage fell below the pre-specified 90 and 95% targets, while uncertainty-based abstention reduced error relative to matched-random rejection in most recorded repeats. Functional profiles were less predictive, although more functional features met the pre-specified high-stability tiers.

DISCUSSION: The tiered features remain stable candidate hypotheses, and raw counts are not directly comparable across the differently sized feature spaces. Adenoma predictions were heterogeneous, and no reviewed external resource met all criteria for formal independent evaluation. CRC-TrustBench separates in-distribution discrimination from cohort generalization and probability reliability without implying clinical deployment or independent external validation.},
}

@article {pmid42857515,
year = {2026},
author = {Karthick, V and Thamarai, R and Amalraj, S and Narayanasamy, K},
title = {Cytopathology of the microbiome-immune interface: Emerging applications of cytology in infectious, inflammatory, and neoplastic conditions.},
journal = {CytoJournal},
volume = {23},
number = {},
pages = {57},
pmid = {42857515},
issn = {0974-5963},
abstract = {OBJECTIVES: The objective of the study is to synthesize current evidence on the microbiome-immune interface as reflected in cytopathologic specimens and to explore the emerging diagnostic, prognostic, and translational applications of cytology in infectious, inflammatory, and neoplastic diseases.

MATERIAL AND METHODS: This narrative review integrates published literature on cytopathology, microbiome research, and immune profiling. Relevant studies examining cytologic specimens, including fine-needle aspiration, effusion cytology, liquid-based cytology, and lavage samples, were evaluated for their contributions to understanding host-microbe interactions. Emphasis was placed on studies incorporating molecular microbiome analysis (16S ribosomal ribonucleic acid sequencing, metagenomics), immunocytochemistry, cytokine profiling, and digital image analysis.

RESULTS: Cytologic specimens provide a minimally invasive platform that captures dynamic interactions between epithelial cells, immune infiltrates, and microbial communities. In infectious diseases, cytology enables direct pathogen visualization while reflecting immune activation patterns such as granuloma formation and neutrophilic inflammation. In chronic inflammatory disorders, cytologic features including lymphoid infiltrates and macrophage activation may correspond with microbiome-driven immune dysregulation. In oncology, tumor-associated microbiota detectable in cytology samples influence immune checkpoint expression, macrophage polarization, and tumor microenvironment remodeling. Integration of molecular assays, single-cell technologies, and artificial intelligence further enhances the ability of cytology to characterize microbiome-immune signatures within limited specimens.

CONCLUSION: Cytopathology is evolving from a purely morphologic discipline into an integrative platform that bridges microbial ecology and immune dynamics. Incorporating microbiome profiling and immune phenotyping into routine cytologic evaluation holds promise for improved disease stratification, early detection, and personalized therapeutic decision-making. Recognizing cytology as a window into the microbiome-immune interface may redefine its role in precision medicine across infectious, inflammatory, and neoplastic conditions.},
}

@article {pmid42857638,
year = {2026},
author = {Chen, J and Jiang, J and Zhou, X and Fan, L and Wu, F and Liang, P and Song, H and Wang, J and Luo, J and Zhu, G},
title = {Characteristics of Microbiota in Different Segments of the Digestive Tract of Orange-Collared Keelback (Rhabdophis himalayanus).},
journal = {Ecology and evolution},
volume = {16},
number = {10},
pages = {e74508},
pmid = {42857638},
issn = {2045-7758},
abstract = {The gastrointestinal tract of animals plays an essential role in digestion and nutrient absorption. The diversity of gut microbiota is critical for maintaining the physiological functions of animals. However, current research has focused primarily on mammals; research on the gut microbiota of reptiles, particularly snakes, remains limited. This study utilized metagenomic sequencing and untargeted metabolomics to investigate the microbial community composition and functional potential in the stomach, large intestine, and small intestine of the Orange-collared Keelback (Rhabdophis himalayanus). The results demonstrate that the three most dominant phyla in the R. himalayanus gut microbiota are Pseudomonadota, Actinomycetota, and Bacillota. Moreover, analysis of microbial communities across the stomach, small intestine, and large intestine shows no significant differences in α-diversity and β-diversity among the three regions. Linear Discriminant Analysis Effect Size (LEfSe) reveals significant differences in the gut microbiota abundance. MetaStats analysis further reveals significant differences in the abundance of both microbial taxa and CAZymes. Although overall metabolite profiles did not differ significantly among gastrointestinal regions, pairwise analyses identified differentially abundant metabolites associated with amino acid, lipid, nucleotide, and cofactor metabolism. Gut microbiota from different parts of the digestive tract may reveal a unique characteristic of the gut microbiome of R. himalayanus and the impact of microbial community structure on function. Collectively, these findings expand our understanding of gastrointestinal microbial communities and associated functional potential in an understudied snake species.},
}

@article {pmid42858079,
year = {2026},
author = {Yang, X and Ye, T and He, Y and Zhao, J and Wang, J and Cheng, X},
title = {Qi-Fu-Yin Attenuates Frailty by Regulating Gut Microbiota and Neuroendocrine Hormones in 5xFamilial Alzheimer's Disease Transgenic Mice.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/73003},
pmid = {42858079},
issn = {1940-087X},
mesh = {Animals ; *Alzheimer Disease/drug therapy/microbiology/blood/metabolism ; Mice, Transgenic ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; *Frailty/drug therapy/microbiology ; Female ; Male ; Disease Models, Animal ; },
abstract = {Frailty is a common and debilitating feature of Alzheimer's disease (AD), yet effective therapeutic strategies targeting both cognitive decline and physical frailty remain limited. Qi-Fu-Yin (QFY), a traditional Chinese herbal formulation, has been used to treat aging-related disorders, but its effects on frailty in AD and the underlying mechanisms are unclear. This study aimed to evaluate whether QFY alleviates frailty in 5xFamilial Alzheimer's Disease (FAD) transgenic mice and to explore the potential involvement of gut microbiota and neuroendocrine hormones. Mice were treated with QFY at low (2.8 g/kg), medium (5.6 g/kg), or high (11.2 g/kg) doses, or with donepezil as a positive control, for 194 days. Frailty-related behaviors were assessed using CatWalk gait analysis, grip strength, rotarod, nest-building, and aging scoring. Plasma hormone levels were measured, and fecal gut microbiota composition and function were analyzed by 16S rRNA sequencing and metagenomic analysis. QFY treatment significantly improved gait parameters, grip strength, motor coordination, nesting ability, and reduced aging scores in 5xFAD mice, with effects comparable to or superior to those of donepezil. QFY also restored aberrant levels of estradiol, testosterone, and corticosterone, and reshaped gut microbiota composition, particularly by increasing the abundance of Adlercreutzia, which negatively correlated with senescence and testosterone levels. Functional metagenomics revealed that QFY partially restored disease-associated microbial pathways, including those involved in carbohydrate metabolism and virulence. These findings suggest that QFY alleviates frailty in 5xFAD mice, with effects associated with concurrent modulation of gut microbiota and neuroendocrine function, though causal relationships require further validation. These findings support further investigation of QFY as a potential intervention for AD-associated frailty.},
}

Animals
*Alzheimer Disease/drug therapy/microbiology/blood/metabolism
Mice, Transgenic
Mice
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/administration & dosage
*Frailty/drug therapy/microbiology
Female
Male
Disease Models, Animal

@article {pmid42858083,
year = {2026},
author = {Zheng, Y and Yang, Y and Mei, X and Guo, T and Gu, L and Liu, X and Yu, J and Yang, X and Yang, M and Li, Y and Zhang, X and Zhou, Y and Zheng, J and Hu, X},
title = {Paired Exploratory Metagenomic Analysis of Gut Microbiota Before and After Ceftizoxime Treatment in College Students with Acute Enteritis.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/71529},
pmid = {42858083},
issn = {1940-087X},
mesh = {Humans ; *Ceftizoxime/therapeutic use/pharmacology/administration & dosage ; Female ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Metagenomics/methods ; Young Adult ; Adolescent ; *Enteritis/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/microbiology ; Students ; Acute Disease ; Metagenome/drug effects ; },
abstract = {This study explored the short-term changes in gut microbiota concurrent with ceftizoxime sodium therapy and clinical recovery in college students with acute enteritis. A retrospective, self-controlled before-and-after design was adopted, enrolling 10 college students (5 males, 5 females; aged 18-24 years) with acute enteritis admitted to Southwest University Hospital. Fecal samples were collected before intravenous antibiotic treatment and at the time of clinical recovery (5-7 days later). All patients received intravenous ceftizoxime sodium (1.0 g every 12 h). Metagenomic sequencing was performed to analyze microbiota composition and diversity. We hypothesized that short-term ceftizoxime therapy would induce detectable species-level restructuring without substantially altering higher-level diversity. Phylum-level analyses showed no statistically significant differences between the two groups. Also, α-diversity analysis at the genus level revealed that the Shannon, Simpson, and Chao1 showed no differences between the two groups (q = 0.054, 0.054 and 0.084, respectively). PERMANOVA based on Bray-Curtis distances at the genus level demonstrated a statistically significant difference in overall microbial community structure between the two groups before and after treatment (F = 1.81, P = 0.043), but no significant difference after adjustment (P = 0.054). ANOSIM performed on the raw full-species abundance table at the species level further detected significant separation between the two groups (R = 0.114, P = 0.016). No species remained statistically significant after false-discovery-rate correction. These exploratory, descriptive findings indicate that species-level temporal changes in the gut microbiota occurred concurrently with ceftizoxime exposure and clinical recovery, but cannot be attributed specifically to the antibiotic. The study provides hypothesis-generating data for future controlled investigations of antibiotic-microbiota interactions in young adults.},
}

Humans
*Ceftizoxime/therapeutic use/pharmacology/administration & dosage
Female
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Metagenomics/methods
Young Adult
Adolescent
*Enteritis/drug therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects/genetics
Feces/microbiology
Students
Acute Disease
Metagenome/drug effects

@article {pmid42858216,
year = {2026},
author = {Khan, A and Ullah, Z and Siraj, M and Younas, S and Wahab, S and Waris, A and Hong, ST},
title = {The Gut Microbiota-Epilepsy Axis: Bibliometric Trends, Mechanistic Insights, and Microbiota-Targeted Next-Generation Therapeutic Opportunities.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42858216},
issn = {1559-1182},
mesh = {Humans ; *Epilepsy/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Brain ; },
abstract = {Epilepsy is a complex neurological disorder with diverse underlying causes. Growing evidence suggests that gut dysbiosis may promote epileptogenesis by disrupting short-chain fatty acids, tryptophan-kynurenine metabolism, immune signaling, and neuronal excitability. In this review, we combine findings from human and animal studies to explain how gut dysbiosis may influence seizures through the gut-brain axis. We highlight emerging and less-discussed mechanisms, including vagus nerve signaling, microbial amyloids, bacterial extracellular vesicles (BEVs), the queuosine salvage pathway, and multi-kingdom microbiota interactions. We also summarize microbiota profiling studies and describe dysbiosis patterns linked to seizure. To support translation, we propose a peri-ictal multi-omics strategy for biomarker discovery. This includes standardized sampling and integration of metagenomics, metabolomics, and host transcriptomics. In addition, our bibliometric analysis further shows rapidly growing global interest in this topic. Recent studies increasingly focus on the gut-brain axis, ketogenic diet, and inflammation-driven mechanisms. Finally, we outline both established approaches and emerging next-generation microbiome-based therapeutic strategies, including SCFA-restoring synbiotics, engineered psychobiotics, bacteriophage therapy, and AI-guided personalization. These advances highlight the microbiota as modifiable target for adjunctive epilepsy management and provide a translational roadmap for future mechanistically informed research and clinical interventions.},
}

Humans
*Epilepsy/therapy/microbiology
Animals
*Gastrointestinal Microbiome/physiology
Dysbiosis
Brain

@article {pmid42858339,
year = {2026},
author = {Song, S and Guo, T and You, T and Wang, P},
title = {Diagnosis and treatment of four cases of pulmonary cryptococcosis: case report and literature review.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {9},
pages = {1408-1414},
doi = {10.3855/jidc.20737},
pmid = {42858339},
issn = {1972-2680},
mesh = {Humans ; *Cryptococcosis/diagnosis/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology ; Male ; Antifungal Agents/therapeutic use ; Fluconazole/therapeutic use ; Middle Aged ; *Lung Diseases, Fungal/diagnosis/drug therapy/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Adult ; Tomography, X-Ray Computed ; Aged ; Metagenomics ; Immunocompromised Host ; },
abstract = {INTRODUCTION: Cryptococcosis has attracted global attention due to its high mortality rate, unique geographical distribution, and tendency to cause severe and rapid disease progression. Metagenomic next-generation sequencing (mNGS) is a novel detection technology that provides diagnostic insights for identifying pathogens, particularly rare ones. The present article describes 4 individuals diagnosed with pulmonary cryptococcosis (PC) using mNGS of bronchoalveolar lavage fluid (BALF).

CASE PRESENTATION: Among these patients, 3 had cancer, 1 had sarcoidosis and diabetes, and 2 were exposed to pigeons and/or pigeon droppings. These patients experienced symptoms, including fever, cough, and chest pain. They were diagnosed with PC after mNGS of BALF. The patient was diagnosed based on mNGS test results. Subsequently, the patient was treated with fluconazole, and the patient's chest computed tomography scan showed significant absorption of the lung lesions.

CONCLUSIONS: mNGS of BALF can quickly diagnose PC. This diagnostic method has minimal trauma to the body and is worthy of clinical promotion. Fluconazole remains the preferred and best therapeutic drug for PC treatment.},
}

Humans
*Cryptococcosis/diagnosis/drug therapy
Bronchoalveolar Lavage Fluid/microbiology
Male
Antifungal Agents/therapeutic use
Fluconazole/therapeutic use
Middle Aged
*Lung Diseases, Fungal/diagnosis/drug therapy/microbiology
Female
High-Throughput Nucleotide Sequencing
Adult
Tomography, X-Ray Computed
Aged
Metagenomics
Immunocompromised Host

@article {pmid42858532,
year = {2026},
author = {Paladsing, Y and Linsuwanon, P and Jittmittraphap, A and Leaungwutiwong, P and Morand, S and Chaisiri, K},
title = {Rodent-associated viruses in Asia: ecological drivers, host-virus associations and insights from a systematic review.},
journal = {Research in veterinary science},
volume = {213},
number = {},
pages = {106394},
doi = {10.1016/j.rvsc.2026.106394},
pmid = {42858532},
issn = {1532-2661},
abstract = {Rodent-associated viruses are important zoonotic agents of increasing relevance to public and veterinary health. Muroid rodents occupy diverse natural and human-modified environments, facilitating interactions with humans, livestock and wildlife. However, knowledge of rodent-associated viral diversity and the ecological processes influencing viral maintenance and transmission remains fragmented. This review synthesizes published literature on viral diversity, host-virus associations, research trends, and ecological drivers of viral occurrence in Asian muroid rodents. PubMed and Scopus were systematically searched using terms related to rodents, viruses, and Asian regions. Extracted data included publication characteristics, diagnostic methods, host and virus taxonomy, geography, and ecological metadata. Descriptive analyses, geospatial mapping, and network approaches were applied to identify patterns and knowledge gaps. Of 1,049 records retrieved, 165 studies published between 1968-2025 from 30 Asian countries met the inclusion criteria. These studies documented 106 viral taxa representing 74 genera and 35 families. Research activity increased markedly after 2000 alongside advances in molecular diagnostics and metagenomic sequencing. Studies were concentrated in East and mainland Southeast Asia. Orthohantavirus spp. were the most studied viral group, whereas many other viruses remained poorly characterized. Network analyses identified core murine genera, particularly Rattus, Apodemus, Niviventer, Bandicota and Mus, sharing extensive viral associations. Host age, sex, population density, habitat disturbance, climate, and biodiversity were commonly linked with viral prevalence and dynamics. Despite substantial progress, gaps remain in ecological integration, longitudinal surveillance, and comparative study design. Future research should prioritize standardized, ecologically informed surveillance within an integrated One Health framework to improve zoonotic risk assessment and prevention.},
}

@article {pmid42858585,
year = {2026},
author = {Guo, Y and Xu, T and Yang, Q and Guo, S and Sun, P and Zhou, Y and Wu, X and Chen, Y},
title = {Mechanisms of acid generation and reduction during Jiangxiangxing Baijiu fermentation: insights from practices of raw materials saccharification regulation.},
journal = {Food chemistry},
volume = {532},
number = {Pt 1},
pages = {151434},
doi = {10.1016/j.foodchem.2026.151434},
pmid = {42858585},
issn = {1873-7072},
abstract = {Elevated total acidity in the first round base liquor is a major challenge in Jiangxiangxing Baijiu production. Production practice has shown that enhanced raw material saccharification effectively reduces total acidity. This study investigated the underlying regulatory mechanism. Enhanced saccharification reduced total acidity, predominantly attributable to acetic acid, to 0.059 mol/L, representing a 14.47% reduction, without altering overall microbial succession. Multi-omics and culture-dependent analyses identified Limosilactobacillus panis, Lactobacillus acetotolerans, and Limosilactobacillus avium as core acetic acid-producing microorganisms, with their relative abundances reduced by 48.43%, 43.01%, and 32.67%, respectively. The acetate kinase-mediated pathway was the dominant route of acetic acid biosynthesis, and enhanced saccharification reduced transcription of the acetate kinase-encoding gene. Fermentation validation showed that elevated reducing sugar promoted yeast growth and ethanol production, thereby suppressing acetic acid formation. Overall, enhanced saccharification reduces total acidity in base liquor by modulating reducing sugar-driven microbial dynamics and suppressing acetic acid biosynthesis.},
}

@article {pmid42858690,
year = {2026},
author = {Guler Cekic, S and Vatansever, C and Akpinar, A and Belge, S and Shahrokhi, G and Unal, C and Altintas, A and Aydin, S and Can, F},
title = {Interactions between vaginal, periurethral and urinary microbiota in genitourinary syndrome of menopause and the effects of local estrogen therapy.},
journal = {Maturitas},
volume = {214},
number = {},
pages = {109146},
doi = {10.1016/j.maturitas.2026.109146},
pmid = {42858690},
issn = {1873-4111},
abstract = {OBJECTIVES: Alterations to the vaginal microbiota have been investigated in genitourinary syndrome of menopause but data regarding periurethral and urinary microbiota remain limited. We aimed to characterize vaginal, periurethral, and urinary microbiota in clinically stratified postmenopausal women and to evaluate the effects of estrogen therapy.

STUDY DESIGN: In this prospective study, postmenopausal women were categorized as controls without atrophy or symptoms, women with clinical atrophy without symptoms, symptomatic women, and symptomatic women receiving 12 weeks of vaginal estriol. Vaginal, periurethral, and bladder samples were collected.

MAIN OUTCOME MEASURES: Microbiota composition and diversity (alpha diversity - Shannon index; and beta diversity - Bray-Curtis dissimilarity) across urogenital niches and changes in these following estrogen therapy.

RESULTS: Vaginal and periurethral alpha diversity was higher in women with asymptomatic atrophy and symptomatic women at baseline than in controls and estrogen-treated women. Beta diversity analyses demonstrated separation of controls and estrogen-treated women from the atrophy groups at baseline. Controls exhibited Lactobacillus-enriched periurethral communities and Klebsiella-dominant urinary profiles. Women with asymptomatic atrophy and symptomatic women showed reduced Lactobacillus and increased anaerobic taxa in vaginal and periurethral niches, while urinary samples were characterized by Escherichia predominance. Notably, in women with asymptomatic atrophy, Lactobacillus abundance was higher in periurethral than vaginal samples. Estrogen therapy increased Lactobacillus abundance in vaginal and periurethral compartments and shifted urinary microbiota toward a control-like composition. Periurethral Streptococcus abundance correlated with sexual symptom scores.

CONCLUSIONS: Microbial alterations in genitourinary syndrome of menopause are compartment-specific and extend beyond the vagina. Periurethral microbiota may contribute to symptom expression, while local estrogen therapy promotes restoration of Lactobacillus-dominant urogenital microbiota.

CLINICALTRIALS: gov registration: NCT06633705.},
}

@article {pmid42858715,
year = {2026},
author = {Zhang, X and Zhang, C and Ji, B and Zhang, Z and Xu, C and Cui, T and Chen, L},
title = {Plant litter promotes nitrate-sulfate co-removal in constructed wetlands: DOM dynamics and metagenomic insights into carbon, nitrogen, and sulfur transformations.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131111},
doi = {10.1016/j.jenvman.2026.131111},
pmid = {42858715},
issn = {1095-8630},
abstract = {Plant litter is a low-cost carbon source for constructed wetlands (CWs), but its effectiveness and associated microbial mechanisms in nitrate-sulfate co-contaminated wastewater remains insufficiently understood. This study evaluated cattail and reed litters as in situ carbon sources by integrating substrate characterization, dissolved organic matter (DOM) spectroscopy, microbial community analysis, and metagenomic annotation. Both litter-amended systems effectively promoted simultaneous nitrogen and sulfate removal. The cattail-amended system achieved total nitrogen (TN) removal efficiencies of 73.48%-93.82% and a maximum SO4[2-] removal efficiency of 58.27%, while the reed-amended system achieved 61.10%-91.73% TN removal and 52.90% maximum SO4[2-] removal. DOM optical indices and PARAFAC analysis showed a gradual shift from protein-like to microbial humic-like fluorescence in the cattail-amended system, whereas microbial humic-like fluorescence dominated earlier in the reed-amended system. Metagenomic analysis revealed differences in carbon, nitrogen, and sulfur metabolic potentials. The cattail-amended system showed higher abundances of PPP-related genes associated with NADPH-generating reactions and several denitrification- and sulfur-oxidation-related genes, including narGHI, nirS/K, nosZ, sox, sqr, and fccA/B. The reed-amended system showed higher abundances of selected EMP- and TCA-associated genes and several reductive sulfur genes, including dsr, phs, and ttrABC. The detection of doxD and ttrABC further suggested potential thiosulfate-tetrathionate transformation. Overall, plant litter amendment effectively supported nitrate-sulfate co-removal, while integrated DOM, microbial, and metagenomic analyses revealed different metabolic potentials under cattail and reed amendment.},
}

@article {pmid42858760,
year = {2026},
author = {Yu, C and Wang, Z and Wu, L and Meng, L and Liu, L and Sha, L and Tuo, J and Wang, J and Li, J and Peng, Z and Zhang, Y and Liu, Z and Jin, Z},
title = {Global phylogeography, genomic characteristics and transmission of antibiotic resistance of multi-drug resistant ORN-1-producing Raoultella ornithinolytica B1645-1B.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {106038},
doi = {10.1016/j.meegid.2026.106038},
pmid = {42858760},
issn = {1567-7257},
abstract = {OBJECTIVE: To characterize the genomic phylogeny and antimicrobial resistance (AMR) genotypes of the ORN-1-producing R. ornithinolytica B16451B, and to elucidate the transfer mechanisms of resistance genes at the genomic level.

METHODS: The genome of R. ornithinolytica B16451B was sequenced using the Illumina HiSeq 4000 and PacBio RSII sequencing platforms. A global phylogenetic analysis of the genomic data was conducted by the Center for Genomic Epidemiology (CGE), incorporating information on geographical distribution, isolation sources, and host associations. A comparative phylogenomic analysis was performed using the BLAST Ring Image Generator (BRIG). Genome annotation was performed using Glimmer and the Rapid Annotation using Subsystem Technology (RAST) server. Mobile genetic elements were predicted using TnCentral, ISFinder, and PHASTER. The antibiotic resistance genes (ARGs) were analyzed using the Comprehensive Antibiotic Resistance Database (CARD), while the virulence factors genes (VFGs) were analyzed using the Virulence Factor Database (VFDB). Gene transfer experiments were conducted in the intestinal tract of mice. Transconjugants were identified using 16S rRNA metagenomic sequencing, and drug-resistance genes were amplified by PCR.

RESULTS: A chromosome (designated chromosome 01) was first identified in strain B16451B. A carrying IS4 insertion sequence distinct resistance region within this chromosome, designated B1645-1B-RG, harbors the β-lactamase gene blaORN-1. Three intact prophages, designated prophage YC1, YC2, and YC3, were also first identified. The blaORN-1 gene was successfully transferred from strain B16451B to Escherichia coli (designated B1645-1BLMY1) and Klebsiella pneumoniae (designated B1645-1BYCF2) in the intestines of mice. The strain B16451B harbored 25 antimicrobial resistance genes and 8 classes of virulence factor genes. Based on comparative genomic analysis of strains retrieved from the NCBI Genome Database, 98 antimicrobial resistance genes (ARGs) (e.g., sul1, blaKPC-2, blaNDM-1) among 234 R. ornithinolytica strains were identified to exhibit significantly higher prevalence in human isolates than in non-human host sources (e.g., water, animals, plants).

CONCLUSIONS: The chromosome 01 was identified in a multi-drug resistant ORN-1-producing the strain B16451B isolated from China. The genome of strain B16451B harbors three integrated prophages: YC1 (42.2 kb), YC2 (60.5 kb), and YC3 (23.8 kb) was identified. The IS4 insertion might promote blaORN-1 gene transfer within the intestinal flora of mice. Among these 234 R. ornithinolytica strains analyzed in this study, most virulence factor genes (e.g., ompa, yagx/ecpc) and resistance genes (e.g., blaKPC, blaNDM) exhibited higher prevalence in Homo sapiens isolates than in strains from non-human sources including water, animals and plants. These findings provide valuable references for clinicians optimize the management of R. ornithinolytica infections and guide clinical treatment.},
}