@article {pmid42647600,
year = {2026},
author = {Ottinger, S and Larson, AB and Mercado-Evans, V and Branthoover, H and Zulk, JJ and Serchejian, C and Ogilvie, L and Mejia, ME and Hameed, ZA and Walde, R and Fleck, RC and Ward, CS and Shea, AE and Patras, KA},
title = {Urogenital immune signatures are associated with birth outcomes after maternal urinary tract infection.},
journal = {Science translational medicine},
volume = {18},
number = {864},
pages = {eaea1228},
doi = {10.1126/scitranslmed.aea1228},
pmid = {42647600},
issn = {1946-6242},
mesh = {Female ; Animals ; *Urinary Tract Infections/immunology/microbiology/complications ; Pregnancy ; Humans ; Cytokines/blood/metabolism ; Premature Birth/immunology/microbiology ; *Pregnancy Outcome ; Male ; Interleukin-10/blood ; *Pregnancy Complications, Infectious/immunology/microbiology ; Mice, Inbred C57BL ; Mice ; Uropathogenic Escherichia coli ; Th17 Cells/immunology ; },
abstract = {Preterm birth is the leading cause of infant mortality, resulting in more than 1 million neonatal deaths globally each year. Maternal urinary tract infection (UTI) during pregnancy increases risk for preterm birth; however, biological processes mediating UTI-associated preterm birth are not well described. We established a murine maternal UTI model in which challenge with uropathogenic Escherichia coli (UPEC) initiated preterm labor and birth in about half of dams. Although bacterial burdens were similar, dams experiencing preterm birth displayed excessive bladder inflammation, elevated placental and decidual cytokines, higher proportions of male fetuses, and lower maternal serum interleukin-10 (IL-10) compared with nonlaboring dams. Exogenous IL-10 or lymph node sequestration of T cells reduced placental type 17 T helper cells (TH17 cells) and abrogated preterm birth. In a human pregnancy cohort, we correlated urinary cytokines with birth outcomes and urine culture status. These analyses yielded an exploratory, noninvasive culture-agnostic system for evaluating preterm birth risk, implicating T cell-related cytokines including IL-10, IL-15, GM-CSF, and RANTES. These findings demonstrate that our murine model provides a platform to investigate immunological and microbial factors governing UTI-associated preterm birth and, coupled with patient samples, may be used to identify candidate biomarkers and mechanistic targets for future investigation.},
}

Female
Animals
*Urinary Tract Infections/immunology/microbiology/complications
Pregnancy
Humans
Cytokines/blood/metabolism
Premature Birth/immunology/microbiology
*Pregnancy Outcome
Male
Interleukin-10/blood
*Pregnancy Complications, Infectious/immunology/microbiology
Mice, Inbred C57BL
Mice
Uropathogenic Escherichia coli
Th17 Cells/immunology

@article {pmid42648171,
year = {2026},
author = {Maria, CRC and Estrada, CSD and Mattsson, HK and de Oliveira, OA and de Oliveira de Paiva Gil, C and de Rezende, CE and Lopes, TAC and Lopes, RS and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F},
title = {Co-occurrence of muddy off flavor and cyanotoxin genes in the polluted Guandu river waters (Rio de Janeiro, Brazil).},
journal = {The Science of the total environment},
volume = {1050},
number = {},
pages = {182176},
doi = {10.1016/j.scitotenv.2026.182176},
pmid = {42648171},
issn = {1879-1026},
abstract = {The Guandu river basin is responsible for supplying Rio de Janeiro municipality, Brazil, with drinking water. This study investigated water quality during the geosmin crisis in January and March 2020, by relating the water quality and odor compounds with metagenomic tools. Guandu river water was eutrophic. The cyanobacterial genera identified were Microcystis, Planktothrix, Dolichospermum, Nostoc, Synechococcus, Planktothricoides, and Cyanobium, indicating that bloom-associated communities in the system are taxonomically diverse. Functional annotation of metagenomic sequences revealed the presence of genes associated with the biosynthesis of taste-and-odor compounds, including geosmin (geoA) and 2-methylisoborneol (mic), as well as multiple biosynthetic clusters related to cyanotoxin production. Genes linked to microcystin (mcy), saxitoxin (sxt), anatoxin (ana), cylindrospermopsin (cyr), lyngbyatoxin (ltx), guanitoxin (gnt), and nodularin (nda) were detected across the dataset, indicating a broad genetic potential for the production of secondary metabolites relevant to water quality. The co-occurrence of cyanotoxins, geosmin and 2-MIB genes suggests that off-flavor is an indication of cyanotoxin potential production in the water.},
}

@article {pmid42648179,
year = {2026},
author = {Liu, Y and Li, X and Su, J and Bai, Y and Wang, Y and Li, X},
title = {Simultaneous removal of nitrogen, Cu[2+], and bisphenol A in a hydrogel-biochar-AQDS immobilized bioreactor with added bicarbonate: Performance and metagenomic insights.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143395},
doi = {10.1016/j.jhazmat.2026.143395},
pmid = {42648179},
issn = {1873-3336},
abstract = {As the complexity of industrial wastewater pollution continues to increase, the simultaneous removal of nitrogen, metal contaminants, and persistent organic pollutants under low carbon conditions has become a key challenge for biological treatment systems. To address the operational instability and dependence on carbon sources observed in immobilized systems when exposed to copper (Cu[2+]) and bisphenol A (BPA), the Pseudoalteromonas japonicus strain LY0623 was integrated into a hydrogel-biochar-AQDS composite carrier to construct a multifunctional immobilized biofilm system. Notably, under conditions containing only NaHCO3, the R4 system achieved an NH4[+]-N removal rate of 89%. Under conditions where Cu[2+] and BPA coexist, the R4 system achieved removal of NH4[+]-N (89%), NO3[-]-N (100%), Cu[2+] (85%), and BPA (88%). Sediment characterization confirmed that Cu[2+] was immobilized through adsorption, complexation, and microbiologically induced carbonate precipitation (MICP). Metagenomic analysis further indicated that the Pseudomonadota phylum remained the dominant phylum, while functional pathways associated with inorganic carbon assimilation, HNAD nitrogen metabolism, endogenous carbon transformation, biomineralization, electron transfer, and aromatic compound degradation were preserved. By combining ammonia oxidation driven energy production, inorganic carbon utilization, redox mediated processes, and biomineralization, this study provides a highly promising low carbon strategy for treating industrial wastewater containing mixed pollutants.},
}

@article {pmid42648218,
year = {2026},
author = {González-Camacho, F and Ruiz-Rodriguez, P and González, I and Guerrero-Vadillo, M and Coscollá, M and González-Rubio, JM},
title = {Agricultural sprinkler irrigation systems as environmental reservoirs and airborne dissemination sources of Legionella pneumophila.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130797},
doi = {10.1016/j.jenvman.2026.130797},
pmid = {42648218},
issn = {1095-8630},
abstract = {Sprinkler irrigation systems are critical for modern agriculture but represent largely unrecognized aquatic environments capable of sustaining opportunistic human pathogens. Among them, Legionella pneumophila is of particular concern due to its ability to colonize engineered water systems, persist under fluctuating environmental conditions, and be transmitted through aerosols. In this study, we conducted a comprehensive microbiological and genomic investigation of irrigation ponds and ditches in a rural area of north-east Spain where two zones were sampled. Metagenomic profiling revealed highly diverse microbial communities encompassing more than 20,000 species, including 21 airborne-transmissible bacterial pathogens of clinical relevance. Notably, L. pneumophila was detected in both zones, with a relative abundance of up to 4.6 %. Culture-based isolation confirmed the presence of L. pneumophila serogroup 1, Pontiac group, Benidorm subgroup, sequence type 15. Phylogenetic analysis demonstrated a close relationship between this environmental strain and clinical isolates obtained during a Legionnaires' disease outbreak occurred in 2015, which had remained without a confirmed environmental source. Meteorological data from the exposure period revealed wind conditions favouring long-distance aerosol dispersion from irrigated fields toward residential areas. Our findings provide evidence that irrigation infrastructures can act as environmental reservoirs and dissemination routes of L. pneumophila among other airborne pathogens. These results underscore the need to incorporate agricultural irrigation systems into routine environmental surveillance, outbreak investigations, and public health risk assessments.},
}

@article {pmid42648293,
year = {2026},
author = {Oka, A and Bongers, G and Mishima, Y and Baltus, AJ and Gray, SM and Liu, B and Herzog, JW and Benedetto, JR and Fan, TJ and Jang, J and Awoniyi, M and Rousta, E and Hao, LY and Gharaibeh, RZ and Fodor, AA and Ohkusa, T and Atarashi, K and Fukuda, S and Honda, K and San Mateo, LR and Sartor, RB},
title = {Defined human Clostridia consortia reverse colitis via dual effects of tryptophan metabolites on microbiota and immunity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.08.003},
pmid = {42648293},
issn = {1934-6069},
abstract = {Microbial dysbiosis and disrupted mucosal immune homeostasis are integrally involved in the pathogenesis of inflammatory bowel diseases (IBDs). Live biotherapeutic products (LBPs) offer a potential therapeutic strategy to restore beneficial microbes and mitigate disease. We investigated the therapeutic efficacy of 2 LBPs, human Clostridia consortia 17-mix and 11-mix, by treating established colitis in murine models. Both LBPs exhibited therapeutic effects in T cell-mediated chronic colitis models induced by human microbiota and in pathobiont-driven gnotobiotic colitis models established with combinations of IBD-relevant human-derived strains. Metagenomic and metabolomic analyses elucidated mechanisms that go beyond established functions driven by short-chain fatty acids (SCFAs) and interleukin (IL)-10-producing regulatory T cells. Notably, LBPs exerted therapeutic effects by directly inhibiting resident pathobionts and through IL-10-independent activation of host anti-inflammatory aryl hydrocarbon receptor (AhR) pathways by bacterial tryptophan metabolites. These results elucidate SCFA- and IL-10-independent protective mechanisms exerted by defined resident bacterial strains that are depleted in IBD dysbiosis.},
}

@article {pmid42648688,
year = {2026},
author = {Tang, Y and Wang, S and Wang, D and Li, J and Yan, W},
title = {Temperature Sensitivity of Pyrrhotite-Driven Metavanadate Bioreduction in Groundwater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125571},
doi = {10.1016/j.envres.2026.125571},
pmid = {42648688},
issn = {1096-0953},
abstract = {Pyrrhotite-driven metavanadate [V(V)] bioreduction is a promising green strategy for the remediation of vanadium-contaminated aquifers. However, how this microbially driven process responds to different temperatures remains unclear. Herein, the responses of pyrrhotite-driven V(V) bioreduction to different temperatures ranging from 4 to 45 °C were investigated. V(V) removal first increased and then decreased with increasing temperature, peaking at 35 °C, with the reaction rate constant reaching 0.077 d[-1]. V(V) could be reduced to VO2 precipitates, accompanied by oxidation of S(-II) and Fe(II) to sulfate and Fe(III), respectively. Metagenomic binning revealed that S(-II) oxidation was more sensitive to temperature changes than Fe(II) oxidation for V(V) reducers. Bacteria coupling V(V) reduction with both S(-II) and Fe(II) oxidation (e.g., Ramlibacter sp.) were detected exclusively at 35 °C. The transcription of functional genes (related to V(V) reduction, S(-II) oxidation, and Fe(II) oxidation), electron transport activity and related components all exhibited a temperature-dependent pattern, first increasing and then decreasing, with a peak at 35 °C. This study reveals the temperature sensitivity of pyrrhotite-driven V(V) bioreduction, which is helpful for risk assessment and targeted bioremediation of vanadium contamination under different temperature conditions.},
}

@article {pmid42649294,
year = {2026},
author = {Sichert, A and Pollak, S and Priest, T and Goyal, A and Miravet-Verde, S and Sunagawa, S and Cordero, OX and Sauer, U},
title = {Synergistic degradation of fucoidans in the ocean.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42649294},
issn = {1476-4687},
abstract = {Fucoidans, a class of complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration owing to their resistance to microbial degradation[1,2]. Although individual microorganisms can break down portions of these polysaccharides[3-5], it remains unclear whether complete breakdown is possible in nature and, if so, by what mechanisms. Here we show that fucoidans are degraded through synergistic interactions between specialized bacteria with complementary metabolic functions. Using metabolomic analysis of a reconstructed marine consortium, we uncovered metabolic guilds of bacteria that preferentially degrade either the sulfated fucose backbone or the side branches of rare monomers. This functional division of labour leads to an unexpectedly high number of synergistic interactions between different degraders that enhanced degradation efficiency up to 97.1%. Despite varying fucoidan structures across different types of algae[6], the metabolic functions of degraders remained conserved, enabling quantitative prediction of degradation outcomes based on community and substrate composition. The frequent co-occurrence of functionally complementary fucoidan degraders in ocean metagenomes suggests that synergistic degradation is a globally relevant strategy. Our findings suggest that the environmental turnover of complex biopolymers depends not only on individual metabolic capabilities of degraders but also on ecological interactions shaped by substrate architecture. This work provides a mechanistic framework for understanding carbon cycling in the ocean and for engineering synthetic microbial consortia to degrade recalcitrant polysaccharides.},
}

@article {pmid42649853,
year = {2026},
author = {Boldeanu, L and Ghenea, AE and Plasiciuc, AEC and Boldeanu, MV and Pădureanu, R and Assani, MZ and Pădureanu, V and Siloși, I and Novac, MB and Camen, AB},
title = {Gut Microbiome-Driven Strategies to Overcome Immunotherapy Resistance in Microsatellite-Stable Colorectal Cancer.},
journal = {Cancers},
volume = {18},
number = {16},
pages = {},
doi = {10.3390/cancers18162538},
pmid = {42649853},
issn = {2072-6694},
support = {//University of Medicine and Pharmacy/ ; },
abstract = {BACKGROUND/OBJECTIVES: Microsatellite-stable colorectal cancer (MSS CRC) accounts for the vast majority of CRC cases and remains largely resistant to immune checkpoint inhibitors. Emerging evidence suggests that the gut microbiome is an important regulator of antitumor immunity and may contribute to immunotherapy resistance through multiple mechanisms involving the tumor microenvironment. This review aims to summarize current knowledge of the microbiome-immunity-therapy axis in MSS CRC and to explore microbiome-based strategies to enhance immunotherapy responsiveness.

METHODS: A narrative review of the recent literature was conducted, focusing on studies published within the last five years that investigated gut microbiota composition, microbial metabolites, tumor immune regulation, immunotherapy response, and microbiome-targeted therapeutic interventions in CRC. Evidence from mechanistic studies, translational research, clinical investigations, and multi-omics analyses was integrated.

RESULTS: Current evidence indicates that gut dysbiosis contributes to immune resistance in MSS CRC through immune exclusion, myeloid-driven immunosuppression, T-cell dysfunction, chronic inflammation, and altered microbial metabolite signaling. Specific microorganisms, including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, pks-positive Escherichia coli, and other CRC-associated pathobionts, have been implicated in tumor progression and modulation of antitumor immunity. Microbial metabolites such as short-chain fatty acids, tryptophan-derived compounds, bile acids, succinate, and inosine represent key functional mediators linking microbial communities to host immune responses. Emerging microbiome-targeted interventions, including fecal microbiota transplantation, next-generation probiotics, postbiotics, selective microbial depletion, and engineered bacterial therapeutics, have shown promising results in preclinical models and early translational or clinical studies, although robust clinical evidence remains limited. In parallel, advances in metagenomics, metabolomics, spatial transcriptomics, and artificial intelligence are facilitating the development of precision immuno-microbiome oncology approaches.

CONCLUSIONS: The gut microbiome functions as a critical regulator of immune resistance in MSS CRC through coordinated effects on microbial composition, metabolite production, and tumor immune remodeling. Microbiome-targeted interventions, combined with multi-omics-based patient stratification, may provide new opportunities to overcome immunotherapy resistance and expand the clinical benefits of immune checkpoint blockade in this traditionally refractory disease.},
}

@article {pmid42649929,
year = {2026},
author = {Cathomas, M and Fortunato, F and Zamir, E and Keller, MI and Gobin, T and Jötten, L and Gauer, E and Heckler, M and Kong, B and Gaiser, RA and Rompen, IF and Harnoss, JM and Schmidt, S and Kuhn, M and Elinav, E and Bork, P and Michalski, CW and Hank, T},
title = {Tumor Location and Preoperative Biliary Stenting Shape Gut Microbiome Diversity in Pancreatic Cancer.},
journal = {Cancers},
volume = {18},
number = {16},
pages = {},
doi = {10.3390/cancers18162617},
pmid = {42649929},
issn = {2072-6694},
abstract = {Background: Recent evidence suggests that gut microbiome plays a role in the development of pancreatic ductal adenocarcinoma (PDAC) and influences treatment response. However, the association of tumor location and preoperative biliary stenting (PBS) with gut microbial composition and diversity remains poorly understood. Methods: Preoperative stool specimens were prospectively collected from patients with PDAC undergoing surgery between March 2020 and July 2021 at the Department of Surgery, Heidelberg University Hospital, Germany. Whole-genome shotgun metagenomic sequencing was performed. Microbial diversity was assessed using the Shannon index and Bray-Curtis dissimilarity with principal coordinates analysis. Results: A total of 63 preoperative stool samples were analyzed from 40 patients with pancreatic head (63.5%) and 23 with body/tail tumors (36.5%). Baseline characteristics were comparable between groups. Microbial community composition differed significantly between tumor locations (Bray-Curtis, p = 0.005), with enrichment of Ruminococcus bromii in body/tail tumors. Among patients with pancreatic head tumors, PBS was associated with reduced alpha diversity (Shannon index, p = 0.04) and depletion of taxa including Eubacteriales and Clostridiales taxa, and members of the genera Raoultella and Prevotella. PBS was associated with a higher rate of major complications > 3a according to the Clavien-Dindo classification (28.6% vs. 3.8%; p = 0.04). Conclusions: PBS was associated with reduced microbial diversity and distinct taxonomic alterations of the gut microbiome. These findings suggest that biliary stenting is associated with microbiome alterations that may be relevant for perioperative risk stratification and warrant further investigation.},
}

@article {pmid42650230,
year = {2026},
author = {Smirnova, YD and Sabler, P and Weidinger, A and Grillari, J and Dungel, P and Kozlov, AV},
title = {Keratinocytes with DNA Aberration Induced by UVB Become Susceptible to Ferroptosis.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antiox15080966},
pmid = {42650230},
issn = {2076-3921},
abstract = {Keratinocytes are key epidermal cells that are highly susceptible to ultraviolet (UV)-induced damage, which can lead to DNA mutations and the development of malignancies. In parallel, UV radiation induces lipid peroxidation (LPO), potentially facilitating the activation of ferroptosis, a form of programmed cell death. We hypothesized that UV-mediated DNA damage, resulting in the formation of cyclobutane pyrimidine dimers (CPDs), occurs preferentially in cells with elevated LPO levels, and that mild induction of ferroptosis in proliferating keratinocytes selectively eliminates cells with high CPD levels. A human keratinocyte cell line was exposed to UVB radiation and subsequently treated with the ferroptosis inducers RSL3 and erastin. Cell death was assessed using LDH analysis, LPO was measured using the fluorescent probe BODIPY™ 581/591 C11, and CPD formation was quantified by ELISA. Using different doses of UVB, we confirmed UVB irradiation simultaneously increases the cell death rate and LPO and CPDs levels in proliferating keratinocytes. Mild induction of ferroptosis in these cells led to a slight increase in the cell death rate and simultaneously to a drastic reduction in CPD levels, suggesting that there is a specific pool of cells predominantly susceptible to UVB in terms of DNA damage and LPO induction. Our findings support our hypothesis that induction of ferroptosis in proliferating keratinocytes exposed to UVB radiation preferentially eliminates cells with elevated CPD levels and may therefore serve as a protective mechanism against UV-induced carcinogenesis.},
}

@article {pmid42650281,
year = {2026},
author = {Gashi, N and Dávid, P and Mikolás, M and Fauszt, P and Gál, F and Rácz, C and Molnár, K and Stündl, L and Remenyik, J and Dobos, AC and Paholcsek, M},
title = {Land-Use and Depth-Dependent Assembly of Soil Microbiomes Shapes Ecological Functions, Interaction Networks, and Phytopathogenic Communities Across Crop and Orchard Systems.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antiox15081017},
pmid = {42650281},
issn = {2076-3921},
abstract = {Soil microorganisms are essential for nutrient cycling, plant productivity, and soil health, yet the relative importance of land-use and soil depth in shaping agricultural microbiomes remains poorly understood. This study investigated soil microbial communities across uncultivated land, alfalfa fields, crop systems (feed corn and sweet corn), and orchard systems (walnut and quince) in the Hajdúnánás region of Hungary using shotgun metagenomic sequencing and soil physicochemical analyses. Microbial alpha diversity showed limited variation among land-use systems but declined significantly with soil depth in both bacterial (Kruskal-Wallis, p = 0.00054) and fungal (p = 0.00051) communities. Beta diversity analyses identified soil depth as the primary driver of microbial community composition in both bacterial (R[2] = 0.305, p = 0.001) and fungal (R[2] = 0.277, p = 0.001) communities. In contrast, land-use significantly influenced only fungal community composition (R[2] = 0.250, p = 0.005). Fungal alpha diversity showed significant negative relationships with soil pH and CaCO3, whereas bacterial diversity exhibited only weak correlations. Crop soils contained the highest numbers of unique bacterial and fungal taxa. Functional analyses revealed significant differences in nutrient cycling, plant-growth-related, decomposition, and environmental adaptation functions among land-use systems. In crop soils, topsoil communities were enriched in oxidative stress-related pathways involved in reactive oxygen species detoxification (ROS), redox homeostasis, and stress regulation, whereas subsoil communities showed a greater representation of antioxidant metabolite production functions. Co-occurrence network analyses indicated greater connectivity in perennial systems, particularly alfalfa soils. Analyses of bacterial and fungal species with reported phytopathogenic potential identified stable cores of phytopathogenic species across agricultural systems, with soil pH emerging as the strongest environmental factor associated with the abundance of phytopathogenic species. Overall, soil depth was the primary driver of bacterial and fungal community assembly, whereas land-use primarily shaped fungal community composition and influenced ecological functions, microbial interaction networks, and the distribution of phytopathogenic species.},
}

@article {pmid42650636,
year = {2026},
author = {Wu, Y and Li, Y and Chen, H and Zhang, X and Song, J and Xia, M and Zheng, Y and Wang, M},
title = {Rare Biosphere Reveals a Decoupling Between Microbial Abundance and Intrinsic Physiological Potential in Shanxi Aged Vinegar Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/foods15162942},
pmid = {42650636},
issn = {2304-8158},
support = {32302034//National Natural Science Foundation of China/ ; 32472324//National Natural Science Foundation of China/ ; 25ZXWCSY00190//Key Research and Development Projects of Tianjin/ ; 25JJJJC0021//Natural Science Foundation of Tianjin/ ; //Innovative Research Team of Shanxi Province/ ; YDZJSX2025D059//Local Science and Technology Development Guided by the Central Government in Shanxi Province, China/ ; },
abstract = {The discrepancy between in situ microbial abundance and actual metabolic performance represents a critical challenge for interpreting microbial function from meta-omic data. Here, we integrated metagenomic and metatranscriptomic sequencing to investigate this decoupling between microbial abundance and cultivation-based physiological potential in Shanxi aged vinegar (SAV) solid-state fermentation. Lactobacillus acetotolerans dominated the community at both the genomic (40.89%) and transcriptomic (55.36%) levels, whereas Pediococcus acidilactici accounted for only 0.11%-a canonical rare-biosphere member. Source tracking via Sankey analysis showed that genes involved in acetate production were primarily attributed to Acetobacter pasteurianus, whereas genes involved in lactate production were predominantly associated with Lactobacillus spp. However, L. acetotolerans exhibited limited acid tolerance and lactic acid production, whereas the low-abundance P. acidilactici AAF1-5 displayed robust stress tolerance and superior lactic acid production under fermentation-relevant conditions-a striking contrast between microbial abundance and physiological performance. Metabolic interaction network analysis predicted that P. acidilactici may be co-inhibited by L. acetotolerans (Ixy = -2.737, resource competition) and A. pasteurianus (Ixy = -1.887, acid stress). To test whether ecological constraints, rather than intrinsic metabolic capacity, underlie this low abundance, we heterologously expressed the heat shock co-chaperone gene grpE from A. pasteurianus in P. acidilactici AAF1-5 as an experimental tool. The recombinant strain P. acidilactici-grpE exhibited significantly enhanced viability under acetic acid stress and, in simulated SAV fermentation, lactic acid content increased by 23.63% compared with the wild-type control. These results demonstrate that meta-omic abundance does not necessarily predict physiological performance and that low abundance may reflect ecological constraints rather than intrinsic functional deficiency. Our study provides an ecological framework for linking microbial abundance with physiological function beyond sequence-based abundance inference in complex fermentation microbiomes.},
}

@article {pmid42650720,
year = {2026},
author = {Kurt, H},
title = {Wastewater Metagenomic Reanalysis of Antibiotic Resistance Genes in Public Datasets from Türkiye (Ankara and Hatay).},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080795},
pmid = {42650720},
issn = {2079-6382},
abstract = {Background/Objectives: Antimicrobial resistance in microbial communities is a global health concern that leads to millions of deaths each year. Many bacterial pathogens have resistance to multiple antibiotics. Domestic wastewater treatment facilities are reservoirs for antibiotic-resistant bacteria and resistance genes. Wastewater-based epidemiology surveillance is crucial for monitoring antibiotic resistance genes (ARGs). Türkiye has one of the highest levels of antibiotic resistance with a lack of research on resistomes. This study is a focused reanalysis of publicly available wastewater metagenomes from Türkiye, comparing them to global and other country's results. Methods: Ten metagenomic data of wastewater treatment from Türkiye were downloaded from NCBI-SRA database. Metagenome assemblies were performed and high-quality metagenome-assembled genomes (HQ-MAGs) were included in the study. Taxonomic annotations and antibiotic resistance profiles were identified in both the metagenome assemblies and HQ-MAGs. Results: A total of 401 different ARGs in 25 antibiotic classes have been identified, including Mcr (including mcr-1, mcr-2, mcr-3 and mcr-5 variants) and optrA. The vanR two-component regulatory system genes for controlling vancomycin antibiotic resistance were one of the most dominant along with other vancomycin resistance genes such as vanA and vanB. A total of 115 HQ-MAGs were obtained with at least eight ARGs. The HQ-MAG with the highest number of resistance genes (58) was found to belong to E. coli. The most frequently encountered resistance genes in HQ-MAGs were the multidrug ABC transporter, vanR, bacA and patA which confer resistance to multidrug, glycopeptide, bacitracin and fluoroquinolone antibiotic groups, respectively. Conclusions: To effectively address the problems of antibiotic resistance outbreaks, comparable AMR surveillance at national and global levels is required for the identification and prioritization of ARGs and resistance genes. This is the first report conducted in Türkiye.},
}

@article {pmid42650728,
year = {2026},
author = {García Gutiérrez, L and Méndez-Tenorio, A and López-Luis, MÁ and Ávila-Huerta, SA and León-Ávila, G and Castaño-Valencia, SR and Ibáñez-Cervantes, G},
title = {Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080804},
pmid = {42650728},
issn = {2079-6382},
support = {SECHITI CBF-2025-I-2588//Secretaría de Ciencia Tecnología e Innovación/ ; },
abstract = {The resistome, defined as the complete set of antibiotic resistance genes (ARGs) present in the microbiota of a given environment, is a critical component for understanding the evolutionary dynamics of antimicrobial resistance (AMR) and its impact on human, animal, and environmental health. This review summarizes current methods and technological advances and offers a forward-looking perspective on resistome research. A systematic literature search was conducted. References on short-read and long-read sequencing, amplicon sequencing, shotgun metagenomics, and multi-omics integration were included, as were bioinformatics tools for the detection, quantification, and annotation of ARGs. The results indicate that next-generation sequencing (NGS) technologies have significantly improved the characterization of ARGs across ecosystems, enabling high-resolution microbial profiling and the discovery of new variants. Furthermore, integrating multi-omics approaches with computational tools improves data accuracy, reduces analysis and reporting times, and facilitates the development of predictive models. However, significant challenges remain, which will be key to strengthening epidemiological surveillance under the One Health approach.},
}

@article {pmid42651016,
year = {2026},
author = {Wu, H and Zhang, P and Li, S and Zhao, H},
title = {Next-Generation Sequencing in Melioidosis: Enhancing Diagnosis, Epidemiology and Antimicrobial Resistance Surveillance.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {16},
pages = {},
doi = {10.3390/diagnostics16162613},
pmid = {42651016},
issn = {2075-4418},
support = {XSTS2025105//Hainan Medical University/ ; ZDYF2022SHFZ050//Department of Science and Technology of Hainan Province/ ; },
abstract = {Melioidosis, caused by Burkholderia pseudomallei, is a severe infectious disease with high mortality. Diagnostic delays due to conventional culture and serology limitations impact patient outcomes. This narrative review synthesizes evidence on next-generation sequencing (NGS) in melioidosis. NGS technologies encompass two main applications: metagenomic NGS (mNGS), which enables culture-independent detection directly from clinical samples, and whole-genome sequencing (WGS), which provides outbreak tracing and source attribution from cultured isolates. Resistance profiling detects antimicrobial resistance (AMR) determinants (e.g., penA mutations) to guide therapy. Recent 2025-2026 studies highlight new applications, including direct pathogen genome recovery from environmental samples. Despite cost and standardization challenges, integrating NGS into clinical workflows holds promise for improving melioidosis management, especially in resource-limited settings.},
}

@article {pmid42651144,
year = {2026},
author = {Lee, S and Hong, SH and Nam, YJ and Cho, YH and Son, SJ and Hong, CH},
title = {An Integrated Model Based on Gut Microbiota and APOE Genotype for Predicting Dementia Risk.},
journal = {Brain sciences},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/brainsci16080834},
pmid = {42651144},
issn = {2076-3425},
support = {6637-303//Korea Disease Control and Prevention Agency/ ; RS-2025-25303051//Korea Health Industry Development Institute/ ; RS-2022-KHI30309//Korea Health Industry Development Institute/ ; GRRCAjou2023-B02//Gyeonggi Provincal Medical Center/ ; RS-2021-NR056488//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Dementia develops through the combined influence of genetic vulnerability, biological processes, and environmental exposures. The apolipoprotein E (APOE) ε4 allele is a well-known genetic contributor to dementia risk, and growing evidence links gut microbial alterations to cognitive decline and cerebrovascular-related pathology. Nevertheless, studies jointly evaluating genetic, microbiome, and clinical information remain relatively scarce. This study examined an integrated framework combining APOE genotype and gut microbiome data for cross-sectional dementia classification.

METHODS: We analyzed 292 participants representing three cognitive stages: subjective memory impairment (SMI), mild cognitive impairment, and dementia. Clinical variables, APOE genotype, and gut microbial metagenomic profiles were examined. Associations among genetic risk, Alzheimer's disease pathology, and brain structural changes were assessed, and multivariable models were used to distinguish participants with dementia from those with SMI or MCI.

RESULTS: APOE ε4 carriage was most frequent among participants with dementia, while no ε4 carriers were observed in the SMI group. Gut microbial profiles differed according to the dementia-related genetic-risk category (mild vs. moderate-to-high). The fully integrated model showed a numerically higher cross-validated AUC than models constructed from fewer data domains. Streptococcus, Akkermansia, and Fusicatenibacter were more abundant in the moderate-to-high genetic-risk group; these taxon-level findings were exploratory and based on nominal p-values.

CONCLUSIONS: The findings support an exploratory integrated framework for cross-sectional dementia classification based on genetic and gut microbiome information. Independent longitudinal and multicenter validation is required before the framework can be interpreted as predicting future dementia risk or supporting personalized clinical decisions.},
}

@article {pmid42651677,
year = {2026},
author = {Liu, M and Wang, Z and Zhu, R and Xie, H and Wanghe, K},
title = {Microbial Functional Potentials Differ Among Monospecific and Mixed Moss Biocrusts in an Alpine Sandy Ecosystem.},
journal = {Biology},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/biology15161372},
pmid = {42651677},
issn = {2079-7737},
support = {2026-HZ-804//The Science and Technology Department of Qinghai province/ ; 32260284//the National Natural Science Foundation of China/ ; },
abstract = {Moss-dominated biological soil crusts are associated with carbon and nitrogen cycling in dryland and alpine sandy ecosystems, but functional differentiation among closely related moss species and their mixed assemblages remains unclear. We used shotgun metagenomic sequencing to compare below-crust soil associated with Didymodon constrictus (Mitt.) K. Saito (D. constrictus) crusts (mossC), ferrugineus (Schimp. ex Besch.) M.O. Hill (D. ferrugineus) crusts (mossF), and visually co-dominated mixed crusts (mossM) in the Gonghe Basin on the northeastern Qinghai-Tibet Plateau. Fifteen spatially separated quadrats per category were pooled into three composite biological replicates (effective n = 3). KEGG, CAZy, and targeted carbon- and nitrogen-cycling annotations showed category-associated differences in relative gene representation. MossC had greater mean representation of glycoside hydrolases and several complex-carbon-processing functions, mossF had greater representation of nitrogen-assimilation and acetate-related functions, and mossM had greater representation of selected carbon-degradation, nitrogen-mineralization, and dissimilatory-nitrate-reduction functions. The full RDA model explained 58.4% of functional variation (adjusted R[2] = 0.334; exact permutation p = 0.028340), with single-variable associations retained for total carbon and soil water content. Genus-level taxonomic dissimilarity correlated with KEGG, CAZy, carbon-cycling, and nitrogen-cycling dissimilarities after FDR correction. MossM showed both positive and negative descriptive deviations from the approximate unweighted midpoint of mossC and mossF, but no inferential test was applied to these deviations. The small number of composite replicates, visually estimated moss proportions, edaphic confounding, and absence of activity measurements limit causal and confirmatory interpretation.},
}

@article {pmid42651792,
year = {2026},
author = {Kuchaka, DJ and Shayo, MJ and Beti, M and Kimu, P and Wadugu, BD and Ignass, IP and Phares, G and Juma, MA and Kumburu, HH and SeqTZ Consortium, and Kazyoba, PE and Clausen, PTLC and Mmbaga, BT and Mpolya, EA and Sonda, TB},
title = {Metagenomic Profiling of Diarrheagenic Escherichia coli Pathotypes Reveals Predominance of Diffusely Adherent and Enteroaggregative Subtypes and Mixed Signatures Among Under-Fives in Tanzania.},
journal = {Current issues in molecular biology},
volume = {48},
number = {8},
pages = {},
pmid = {42651792},
issn = {1467-3045},
support = {20-12-TAN//Ministry of Foreign Affairs of Denmark/ ; },
abstract = {Diarrheagenic Escherichia coli (DEC) is a leading enteric pathogen in children under five in sub-Saharan Africa, yet conventional targeted assays fail to capture mixed virulence signatures or provide quantitative context relative to E. coli carriage. We applied a virulence-aware nanopore metagenomics workflow to characterise DEC pathotype distribution, mixed signatures, and virulence gene burden in 126 under-five stool metagenomes from six Tanzanian regions. Virulence support was quantified as aligned bases normalised to per-sample E. coli-aligned bases, termed GPMB (gene bases per million E. coli-aligned bases). At least one DEC virulence family was detected in 79/126 (62.7%) samples. afa/dra (diffusely adherent E. coli [DAEC] marker) was the most prevalent family (46/126, 36.5%); DAEC-containing pathotypes accounted for 46/79 (58.2%) of all assigned calls across all six regions. Mixed signatures occurred in 21/79 (26.6%) assigned samples, most commonly DAEC + enteroaggregative E. coli (EAEC) (n = 11). Enterotoxigenic E. coli (ETEC) was geographically concentrated in Mwanza. Age-stratified analysis revealed declining DAEC prevalence with age. Multivariable logistic regression found no significant independent associations between DEC positivity and age, sex, or rainfall. Unassigned samples had 6.8-fold lower E. coli carriage depth, implicating sequencing depth rather than pathotype absence as the primary non-detection driver. DAEC and EAEC should be elevated as priority DEC surveillance targets in Tanzania.},
}

@article {pmid42651990,
year = {2026},
author = {Zheng, Y and Wang, W and Yang, H and Wang, Y and Guo, T and Yin, N and Liang, H and Song, B and Jia, Y and Nie, R and Zheng, Y and Gong, R and Qi, J},
title = {Effects of Dietary Dandelion Supplementation on Ruminal Morphology, Fermentation, Microbiome, and Inflammation in Lambs Under High-Concentrate Feeding.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {16},
pages = {},
doi = {10.3390/ani16162585},
pmid = {42651990},
issn = {2076-2615},
support = {2024QN03078//National Natural Science Foundation of Inner Mongolia Autonomous Region/ ; YLXKZX-NND-043//2023 Annual Autonomous Region-Level Institution Talent Introduction Scientific Research Support Project, Inner Mongolia Education Department Special Research Project for First Class Disciplines/ ; NDYB2023-9//Scientific Research Start-up Project for High-Level and Outstanding Doctoral Talents/ ; },
abstract = {This study aimed to investigate the regulatory effects of dietary dandelion supplementation on the ruminal physiological status of lambs fed a high-concentrate diet. Twenty-two 6-month-old female crossbred lambs with an initial body weight of 32.05 ± 0.43 kg were randomly assigned to two groups (n = 11 per group): the HC group (fed a high-concentrate basal diet) and the DD group (basal diet supplemented with 2 g/kg dandelion powder), with a 14-day adaptation and 60-day experimental period. The results showed that compared with the HC group, dandelion supplementation significantly improved lamb growth performance and modulated ruminal fermentation parameters and tissue morphology. For inflammatory indices, the concentration of interleukin-10 (IL-10) was significantly increased, while the concentrations of interleukin-1β (IL-1β), lipopolysaccharide (LPS) and histamine (HIS) were significantly decreased (p < 0.05). Meanwhile, dandelion supplementation upregulated the mRNA expression of ruminal epithelial tight junction proteins and hexokinase II (HK-II), while downregulating the mRNA expression of myeloid differentiation factor 88 (MyD88), voltage-dependent anion channel 1 (VDAC1), inositol 1,4,5-trisphosphate receptor (IP3R), NLR family pyrin domain containing 3 (NLRP3), and caspase-1. Metagenomic analysis revealed that dandelion supplementation did not alter ruminal microbial α-diversity, but slightly modulated community composition and functional profiles. The abundances of dominant phyla Bacteroidota and Bacillota showed only slight fluctuations, while fiber-degrading genera (Xylanibacter, Quinella, Selenomonas) showed a trend toward enrichment, and proteolytic taxa were decreased. CAZyme analysis revealed an upward trend in families CE4, CE8, GH32, and GH13_46 (pectin/starch degradation) and a downward trend in GH73, GH27, and GT14 (oligosaccharide/peptidoglycan/polysaccharide metabolism) in the DD group. KEGG orthology annotation suggested that nominal KO differences were mainly associated with carbohydrate metabolism pathways, including starch and sucrose metabolism and peptidoglycan biosynthesis. None of these features, however, remained significant after FDR correction (raw p < 0.05; all q > 0.05). Collectively, dietary dandelion supplementation was associated with alterations in ruminal physiological status and microbial community in lambs fed a high-concentrate diet, providing foundational data for dandelion application in lamb diets under short-term feeding conditions.},
}

@article {pmid42652023,
year = {2026},
author = {Gajdov, V and Pusic, I and Savic, S and Lazic, G and Zekic, M and Polacek, V and Petrovic, T},
title = {Natural Infection of Domestic Dogs with Raccoon Dog and Fox Amdoparvovirus During a Severe Disease Outbreak.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {16},
pages = {},
doi = {10.3390/ani16162618},
pmid = {42652023},
issn = {2076-2615},
support = {003878144 2025 09418 003 000 000 001 04 004//Provincial Secretariat for Science and Technological Development/ ; 451-03-33/2026-03/200031//Ministry of Science, Technological Development, and Innovation/ ; 101137132//European Commission/ ; },
abstract = {Raccoon dog and fox amdoparvovirus (RFAV) has been reported in raccoon dogs and foxes, but natural infection in domestic dogs has not previously been documented. During March-April 2026, samples from four affected Dobermann dogs from a kennel near Novi Sad, Serbia, were submitted for laboratory investigation. After negative testing for canine adenovirus, canine coronavirus, herpesvirus, parvovirus, distemper virus, influenza A virus, and leptospirosis, metagenomic sequencing was performed on selected tissues, followed by bioinformatic analysis and targeted RFAV PCR screening of additional outbreak-associated samples. Affected dogs had prolonged illness characterized by conjunctivitis with ocular and nasal discharge, occasional blue eye appearance, progressive weight loss, poor coat quality, jaundice and biochemical evidence of hepatic injury, and neurologic signs including paraplegia in advanced cases. Sequencing generated 434,220 reads and identified multiple RFAV hits; pooled assembly produced a 4799 bp consensus genome with approximately 97% similarity to known RFAV strains and genome organization consistent with the genus Amdoparvovirus. RFAV DNA was subsequently detected by virus-specific PCR in an epidemiologically linked dog and across diverse specimen types including blood, urine, kidney, spleen, brain, lung, testicle, ileocecal lymph node, and throat swabs, whereas clinically healthy unrelated dogs were PCR-negative.},
}

@article {pmid42652199,
year = {2026},
author = {Unlu, O and Demirci, M and Kantarci, A},
title = {Role of Oral-Lung Infection Axis on Respiratory Health.},
journal = {Biomedicines},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biomedicines14081817},
pmid = {42652199},
issn = {2227-9059},
abstract = {High-throughput metagenomic sequencing and advances in mucosal immunology have refuted the traditional physiological concept of a sterile respiratory tract. The oral cavity has been recognized as a dynamic determinant of systemic health. As in other parts of the body, recent studies also suggest that pulmonary health may be linked to oral health. Under eubiotic conditions, the oral microbiome maintains local immunological homeostasis and colonization resistance. Oral dysbiosis, characterized by sequential shifts in microbial communities and the proliferation of the pathogenic red complex (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia), induces a state of chronic systemic inflammation, potentially involved in an infectious axis between the oral cavity and the lung. This review evaluates the tripartite systemic pathways of metastatic infection, metastatic injury, and metastatic inflammation that govern the translocation of oral pathobionts and their bioactive components, including lipopolysaccharides, outer membrane vesicles, and matrix metalloproteinases, to the lower respiratory tract via microaspiration and hematogenous circulation. The clinical implications across the chronic respiratory disease spectrum are examined, with a focus on how deficits in oral microbial diversity influence chronic obstructive pulmonary disease (COPD) pathogenesis, modulate the pulmonary virome and mycobiome, and stimulate maladaptive trained immunity. Furthermore, the contribution of biological aging is assessed, highlighting the roles of immunosenescence, inflammaging, and physiological reflex decline within the broader mucosal continuum. Finally, the clinical translation of this axis is analyzed, emphasizing the integration of saliva-based point-of-care nano-theranostics, metatranscriptomic profiling, and targeted interventions-such as professional oral biofilm management in intensive care settings and precision microbiome engineering-to preserve respiratory function and restore immune homeostasis.},
}

@article {pmid42652410,
year = {2026},
author = {Liu, H and Qi, R and Tian, Y and Ren, L and Luo, Y},
title = {Short-Term Feeding on Ecologically Distinct Dietary Plants Is Associated with Gut-Sample Bacterial and Archaeal Profiles in Adult Anoplophora glabripennis.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080756},
pmid = {42652410},
issn = {2075-4450},
support = {32371886//National Natural Science Foundation of China/ ; 2022YFD1401000//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {Ecological control studies of the Asian longhorned beetle (Anoplophora glabripennis) distinguish susceptible, resistant, and dead-end trap trees as functionally different plant categories. We used shotgun metagenomics to examine bacterial and archaeal profiles detected in adult gut samples after 72 h exposure to three dietary plants or prolonged water-only starvation. The study included 24 metagenomes, with three biological replicates per DietGroup × SexGroup combination. No time-zero gut samples were available, so the observed patterns remain superimposed on the beetles' field history. The retained catalogue contained 152,895 bacterial genes and 9 archaeal genes. The original observed-richness difference was strongly correlated with host-depleted read depth and was not supported after common-depth rarefaction. Genus-level Bray-Curtis analysis detected a DietGroup × SexGroup interaction that persisted after depth adjustment and exclusion of low-yield samples. This interaction was exploratory because of the small within-cell sample size. Raw Bray-Curtis analysis of KEGG Orthology profiles showed a DietGroup association, but this association was not robust to direct-depth adjustment or Aitchison analysis. CAZy profiles were descriptive and showed no significant DietGroup effect. These results indicate short-term, depth-sensitive associations between dietary treatment and gut-sample bacterial and archaeal profiles. They do not establish resident status, microbial activity, or a physiological mechanism.},
}

@article {pmid42652934,
year = {2026},
author = {Galisteo, C and Straková, D and García-Roldán, A and de la Haba, RR and Sánchez-Porro, C and Ventosa, A},
title = {The Prokaryotic Community of Hypersaline Soils from the Odiel Saltmarshes: Culturomics Versus Metagenomics.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/life16081246},
pmid = {42652934},
issn = {2075-1729},
support = {PID2023-148654NB-I00//MCIN/AEI/10.13039/501100011033/ ; PID2020-118136GB-I00//MCIN/AEI/10.13039/501100011033/ ; PRE2018-083242//Spanish Ministry of Science and Innovation/ ; P20_01066 and US-1263771//Junta de Andalucía, Spain/ ; FPU20/04312//Spanish Ministry of Universities/ ; },
abstract = {Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes.},
}

@article {pmid42653097,
year = {2026},
author = {Lima, O and Rodríguez-Costas, N and Pérez-Rodríguez, MT and Davina-Nunez, C and Represa, M and Rubiñán, P and Alvarez, M and Ávila-Nuñez, M and Filgueira, A and Portela, C and Sopeña, B and Vasallo Vidal, FJ and Pérez-Castro, S},
title = {KEGG-Based Functional Signatures Complement Taxonomic Profiles Associated with Spontaneous Decolonisation of Carbapenem-Resistant Enterobacterales.},
journal = {International journal of molecular sciences},
volume = {27},
number = {16},
pages = {},
doi = {10.3390/ijms27167092},
pmid = {42653097},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/classification ; *Carbapenems/pharmacology ; *Enterobacteriaceae Infections/microbiology ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; },
abstract = {Understanding the functional potential of the gut microbiota for carbapenem-resistant Enterobacterales (CRE) decolonisation is essential for developing novel non-antibiotic strategies to promote their clearance. In a previous study, we identified distinct taxonomic signatures associated with spontaneous CRE decolonisation (DeCol). Here, we aimed to determine whether these taxonomic differences were accompanied by differences in the predicted functional potential of the gut microbiota. Patients were identified from a database of individuals colonised with CRE. We performed Illumina shotgun metagenomic sequencing on 14 persistent CRE carriage (Col) and 23 DeCol patients with OXA-48-producing isolates. Bioinformatic analysis was performed using SqueezeMeta and differential abundance of functional and metabolic genes was assessed using DESeq2. Several antimicrobial resistance genes, including blaOXA-48, were underrepresented in DeCol patients. In contrast, DeCol patients showed an overrepresentation of genes associated with motility, regulated adhesion, short-chain fatty acid (SCFA)-related pathways and alternative carbohydrate metabolism. These orthologue enrichment patterns are consistent with functions previously linked to intestinal homeostasis in the literature. Conversely, Col patients exhibited an overrepresentation of genes associated with redox defence, biofilm formation and amino acid metabolism, suggesting distinct predicted functional profiles between persistent carriage and spontaneous decolonisation. Spontaneous CRE decolonisation was associated with distinct KEGG-based functional signatures and a lower abundance of antimicrobial resistance determinants. These functional profiles were consistent with the taxonomic differences previously identified in the same cohort and generate hypotheses regarding microbiome functions that may contribute to colonisation clearance. Because these findings are based on gene-content analysis, they reflect predicted functional potential rather than direct evidence of metabolic activity. Further multi-omics and experimental studies are required to validate these observations.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/classification
*Carbapenems/pharmacology
*Enterobacteriaceae Infections/microbiology
Computational Biology/methods
Anti-Bacterial Agents/pharmacology
Metagenomics/methods

@article {pmid42654746,
year = {2026},
author = {Arroyo, JM and Badiali, L and Palmero, D},
title = {Brassicaceae-Based Biosolarization Reduces Lettuce Fusarium Wilt (FOLac) in Naturally Infested Soils.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/pathogens15080810},
pmid = {42654746},
issn = {2076-0817},
support = {PID2021-125545OR-C22//Agencia Estatal de Investigación/ ; },
mesh = {*Fusarium/drug effects ; Soil Microbiology ; *Lactuca/microbiology ; *Brassicaceae/chemistry ; *Plant Diseases/microbiology/prevention & control ; Soil/chemistry ; },
abstract = {Brassicaceae-based bio-disinfestation is a promising non-chemical option to manage lettuce Fusarium wilt caused by Fusarium oxysporum f. sp. lactucae (FOLac), but evidence integrating pathogen suppression, residue chemistry, and soil microbiome response remains limited. We conducted a greenhouse mesocosm assay with naturally infested soil to compare biofumigation (uncovered soil) and biosolarization (plastic-covered soil for 40 days) using five Brassicaceae residues (Brassica carinata, B. juncea, B. napus, Sinapis alba and Raphanus sativus) applied at two field-equivalent doses. Biosolarization created a distinct disinfestation environment, increasing soil temperature by an average of 2.74 °C and shifting oxidation-reduction potential toward reducing conditions. This strategy consistently reduced culturable Fusarium populations, F. oxysporum-assigned colony-forming units (CFU) and lettuce wilt severity compared with uncovered biofumigation. The strongest disease suppression was observed under plastic-covered conditions, including the soil-only control, indicating that the covered microenvironment was a major driver of suppressiveness, while Brassicaceae residues modulated the magnitude and consistency of the response. Glucosinolate profiling revealed contrasting residue chemistries among species, providing a biochemical context for interpreting species-dependent effects. Shotgun metagenomics further showed that biosolarization and biofumigation produced distinct genus-level microbial community structures, with significant effects of strategy, timepoint and their interaction, and higher Shannon diversity under biosolarization. Overall, the integration of disease severity, culture-based inoculum quantification, physicochemical indicators, residue chemistry and metagenomics supports Brassicaceae-based biosolarization as a promising pre-plant approach for suppressing FOLac wilt in naturally infested soils, with the plastic-covered disinfestation environment emerging as the main driver of suppression and Brassicaceae residues modulating the response.},
}

*Fusarium/drug effects
Soil Microbiology
*Lactuca/microbiology
*Brassicaceae/chemistry
*Plant Diseases/microbiology/prevention & control
Soil/chemistry

@article {pmid42654952,
year = {2026},
author = {Wang, J and Wang, K and Yuan, R and Xu, X and Ma, Q and Chen, K and Jiang, Y and He, X and Zhang, X and Liu, X},
title = {Effects of Combined Application of Mushroom Residue and Chemical Fertilizer on Greenhouse Soil Quality and Microbial Community Structure and Function.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081605},
pmid = {42654952},
issn = {2076-2607},
support = {2025QCY KXJ 128//Construction of the "Scientists+Engineers" Team, Shaanxi Qinchuangyuan/ ; },
abstract = {To explore the effects of different fertilization regimes on physicochemical properties and microbial ecology of greenhouse soil, we set five treatments with original soil (BS) as the control: chemical fertilizer alone (GF), high/low-rate mushroom residue combined with chemical fertilizer (MH, ML), and high/low-rate organic fertilizer combined with chemical fertilizer (OH, OL). Metagenomic sequencing and bioinformatic analyses were adopted to characterize soil nutrients, microbial communities, and C-N-P-S metabolic functions. All treatments increased soil nutrients. MH had the highest organic matter, total nitrogen, nitrate nitrogen, and available phosphorus, while GF contained the most available potassium and ammonium nitrogen. Bacteria dominated the soil microbiota, with Pseudomonadota and Pseudomonas as keystone taxa. Mushroom residue amendments improved microbial richness and diversity. By improving soil physicochemical properties, the combined application of organic fertilizer with chemical fertilizer and mushroom residue with chemical fertilizer both enriched some beneficial microorganisms. Chemical fertilizer alone enhanced anaerobic metabolism, which was reversed by high-rate mushroom residue. Available phosphorus, available potassium, and ammonium nitrogen were key environmental factors driving the differentiation of microbial communities and their functions. Overall, mushroom residue combined with chemical fertilizer is effective for greenhouse soil improvement, with proper dosage and tillage recommended.},
}

@article {pmid42654978,
year = {2026},
author = {Kim, M and Koh, YK and Kim, SJ and Min, KH and Ju, HJ and Lee, M and Lee, YB},
title = {Taxonomic and Functional Skin Microbiome Profiles in Nummular Eczema, Atopic Dermatitis, and Mixed Phenotypes: An Exploratory Shotgun Metagenomic Pilot Study.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081631},
pmid = {42654978},
issn = {2076-2607},
support = {None//The Catholic University of Korea Uijeongbu St. Mary's Hospital/ ; IITP-2026-RS-2023-00254592//Institute of Information & Communications Technology Planning & Evaluation/ ; },
abstract = {Nummular eczema (NE) and atopic dermatitis (AD) share clinical features, yet their skin microbiomes remain insufficiently characterized. This exploratory pilot study evaluated the taxonomic composition and functional potential of the skin microbiome across NE, a mixed NE/AD phenotype (Mixed NE_AD), and AD using shotgun metagenomics. Lesional swabs from Korean patients with NE (n = 8), Mixed NE_AD (n = 6), and AD (n = 5) were sequenced to assess microbial diversity, taxonomy, and functional pathways. Staphylococcus aureus predominated across all groups. NE samples were characterized by the higher relative abundance of environmental taxa, wherein Delftia acidovorans was observed only in NE samples in this cohort, and Kocuria palustris diminished sequentially across the Mixed NE_AD and AD phenotypes. Mixed NE_AD exhibited greater intra-genus Staphylococcus diversity. Despite non-significant overall diversity differences, partial ecological separation was noted. Functionally, descriptive differences in metabolic potential were observed, with NE showing trends toward biosynthetic and oxidative stress-associated pathways and AD showing trends toward degradation-related pathways. Mixed NE_AD showed intermediate characteristics. Although these differences did not reach statistical significance after correction for multiple testing, these findings provide preliminary evidence for microbiome-based stratification of eczematous disorders, warranting larger cohort validation.},
}

@article {pmid42654991,
year = {2026},
author = {Kasimanickam, R and Bhowmik, P and Jiang, Z},
title = {Postpartum Uterine Diseases in Dairy Cattle: Integrating Microbiology, Immunology, and Reproductive Physiology.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081645},
pmid = {42654991},
issn = {2076-2607},
support = {GF002076//Population Theriogenology Development Fund/ ; //Department of Veterinary Clinical Sciences, Washington State University/ ; },
abstract = {Postpartum uterine diseases are among the most prevalent and economically important reproductive disorders affecting dairy cattle worldwide. These conditions, including metritis, clinical and subclinical endometritis, and pyometra, develop during the postpartum transition period when physiological, metabolic, endocrine, and immunological adaptations increase susceptibility to microbial invasion and persistent uterine inflammation. Although bacterial contamination of the postpartum uterus is nearly universal, healthy cows generally restore uterine homeostasis through coordinated immune responses, microbial regulation, and effective uterine involution. Failure of these defense mechanisms results in microbial dysbiosis, impaired endometrial repair, reduced fertility, and substantial economic loss. Major pathogens associated with postpartum uterine disease include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, Prevotella spp., and other anaerobic bacteria that interact synergistically to promote inflammation, tissue damage, and reproductive dysfunction. Advances in next-generation sequencing, metagenomics, and metatranscriptomics have transformed understanding of the postpartum uterine microbiota and host-microbe interactions involved in disease pathogenesis. This review synthesizes current evidence regarding uterine physiology, microbial ecology, immune regulation, virulence mechanisms, dysbiosis, diagnostic approaches, and emerging omics-based technologies relevant to postpartum uterine disease in dairy cattle. Particular emphasis is placed on the ecological and physiological interactions linking microbial succession, endocrine recovery, metabolic stress, and immune competence during the postpartum period. The review further discusses translational opportunities for precision diagnostics, microbiome-informed interventions, antimicrobial stewardship, and integrated herd management strategies to improve reproductive efficiency, animal welfare, and dairy herd sustainability.},
}

@article {pmid42654993,
year = {2026},
author = {Li, D and Li, H and Zhang, S and Wu, T and Ye, D and Jin, Y},
title = {Divergent Gut Microbiota Configurations Are Associated with Contrasting Physiological Profiles in Grazing Yaks and Introduced Feedlot Holstein Cattle Under High-Altitude Conditions.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081647},
pmid = {42654993},
issn = {2076-2607},
support = {Grant No. 2024ZD-02//the Major Scientific Research Project of Xizang Vocational Technical College/ ; },
abstract = {The Qinghai-Tibet Plateau presents extreme environmental challenges, including hypobaric hypoxia and nutritional scarcity, to which indigenous yaks (Bos grunniens) are remarkably adapted, whereas introduced Holstein cattle (Bos taurus) often exhibit severe maladaptation. This study compared the gut microbiota of grazing yaks (n = 20) and feedlot Holstein cattle (n = 20) under high-altitude conditions using 16S rRNA gene amplicon sequencing (for community composition) and shotgun metagenomic sequencing (for direct functional profiling of CAZy, COG, and KEGG pathways), combined with in vitro fermentation, digestive enzyme assays, and serum immune- and growth-related indicators. Results: The yak gut microbiota was dominated by Proteobacteria (35 ± 4%) and Actinobacteria (15 ± 2%), whereas Holstein cattle were dominated by Firmicutes (40 ± 4%) and Bacteroidetes (25 ± 3%). At the species level, NR-based metagenomic annotation suggested that Acinetobacter-related taxa, putatively assigned as Acinetobacter pseudolwoffii and A. lwoffii, were abundant in yaks. Functional profiling revealed that the yak microbiota was enriched in CAZy families CE1, GT2, and GT4, whereas the feedlot Holstein cattle microbiota showed enrichment of several KEGG orthologs related to multidrug efflux and carbohydrate transport, including dinF/mepA/vmrA and susC/susD. In vitro fermentation using enriched culturable fecal bacterial consortia showed higher dry matter digestibility and digestive enzyme activities in yak-derived consortia than in Holstein-derived consortia. For serum immune indicators, IgG was significantly higher in feedlot Holstein cattle, whereas IgA and IgM did not differ significantly between groups. Yaks showed higher serum levels of TNF-α, IL-6, TGF-β1, IL-4, IL-10, and IL-13, but lower IL-1β. Conclusions: These findings indicate that divergent gut microbiota configurations are associated with contrasting physiological profiles (e.g., digestive and immune functions) in grazing yaks and introduced feedlot Holstein cattle under the same high-altitude environment. However, due to the confounding effects of diet and management system, causal relationships cannot be inferred from this comparative study.},
}

@article {pmid42654994,
year = {2026},
author = {Sadanov, AK and Baimakhanova, G and Baimakhanova, BB and Orazymbet, S and Ratnikova, I and Smirnova, I and Mamytova, N and Sydykbekova, R and Kossalbayev, BD and Aitkaliyeva, GS and Belkozhayev, AM},
title = {Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081648},
pmid = {42654994},
issn = {2076-2607},
support = {BR28713215//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant-microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly, microbial community functions, plant-microbe communication, and microbiome-mediated stress resistance in agricultural ecosystems. Current approaches to plant-associated soil microbiome manipulation and engineering, including microbial inoculants, synthetic microbial communities (SynComs), microbiome transplantation, rhizosphere steering, and synthetic biology-based interventions, are critically examined. The review further discusses the growing role of metagenomics, metabolomics, metatranscriptomics, machine learning (ML), and precision agriculture technologies in improving microbiome characterization, prediction, and management. Particular attention is given to the application of microbiome-based solutions for sustainable crop production, nutrient management, biological control, climate-smart agriculture, and ecosystem restoration. Despite significant progress, challenges related to field-scale variability, colonization stability, biosafety, regulatory frameworks, and data integration continue to limit large-scale implementation. Future advances in precision microbiome engineering are expected to combine ecological principles, multi-omics technologies, AI, and synthetic biology to develop predictive and resilient microbiome-based solutions for sustainable and climate-resilient agriculture.},
}

@article {pmid42655018,
year = {2026},
author = {Tong, R and An, L and Liang, Z and Wang, Y and Lyu, X and Rong, H and An, Y and Gao, R and Liu, X and Tong, Z and Ren, C},
title = {Integrated Metagenomic and Metabolomic Profiling Identifies Severity-Specific Gut Microbiota Signatures Across A-B-E Phenotypes in Clinically Stable COPD: A Cross-Sectional Study.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081673},
pmid = {42655018},
issn = {2076-2607},
support = {82572469//National Natural Science Foundation of China/ ; 82272187//National Natural Science Foundation of China/ ; 81801935//National Natural Science Foundation of China/ ; 82502615//National Natural Science Foundation of China/ ; GZC20241101//Postdoctoral Fellowship Program of CPSF/ ; Ggyfz202515//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ysbz2025004//Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; BJPSTP-2024-24//Beijing Physician Scientist Training Project/ ; },
abstract = {The ABE classification is crucial for the management of stable chronic obstructive pulmonary disease (COPD), reflecting disease symptom burden and exacerbation risk. Although gut microbiota is intimately linked to COPD pathogenesis, associations among the gut microbiota, its derived metabolites, and exacerbation risk in stable COPD patients remain poorly understood. We recruited 74 stable COPD patients (Group A, n = 18; Group B, n = 26; Group E, n = 30) for cross-sectional multi-omics profiling via fecal metagenomic sequencing and untargeted serum metabolomic analyses. Group E exhibited a decreasing trend in alpha diversity compared to Groups A and B. In addition, Group A displayed the most complex bacterial cooperative network, showing lower complexity and connectivity as symptom burden and risk of exacerbations increased. Taxonomically, the family Prevotellaceae was significantly enriched in Group A, while Streptococcaceae and Lactobacillaceae were more abundant in Groups B and E. Among 51 species displaying progressive trends with increasing exacerbation risk, 35 increased (e.g., Clostridium ljungdahlii) and 16 decreased (e.g., Prevotella dentalis). Furthermore, metabolomics analysis revealed that serum O-phosphoethanolamine levels were markedly elevated in Group E and showed a positive correlation with the COPD Assessment Test and modified Medical Research Council dyspnea scale scores. Exploratory mediation analysis suggested that elevated systemic O-phosphoethanolamine levels partially mediated the association between Clostridium ljungdahlii and COPD exacerbation risk. This study establishes significant associations between gut microbiota and phenotypic stratification in stable COPD patients. The identified Clostridium ljungdahlii/O-phosphoethanolamine axis may be associated with symptom burden and COPD exacerbation risk, provide a basis for further mechanistic studies.},
}

@article {pmid42655034,
year = {2026},
author = {Korotetskiy, I and Shilov, S and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Korotetskaya, N and Tugeyeva, A and Izmailov, T},
title = {Pooled Shotgun Metagenomics Reveals Cloacal Microbiota Composition and Resistome Patterns in Chickens from Kazakhstan.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081689},
pmid = {42655034},
issn = {2076-2607},
support = {AP23485953 - «Epidemiology and molecular biology of avian pathogen resistome»//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Monitoring poultry microbiota and antimicrobial resistance genes is important, as they can reflect flock health, farm conditions, and the level of antimicrobial resistance. Although shotgun metagenomics has been widely applied worldwide to investigate poultry microbiota and antimicrobial resistance, comparable baseline datasets describing the cloacal microbiota and resistome of poultry in Kazakhstan are scarce. In this study, taxonomic and resistome profiles were characterized in pooled metagenomes of the cloacal microbiota of chickens sampled from household and industrial poultry farms in Kazakhstan. Cloacal swabs were collected from laying hens, pooled at the house level, and analyzed using high-throughput metagenomic sequencing. Taxonomic profiles were generated at the genus level, and antimicrobial resistance gene signals were summarized by drug class. Compositional patterns were assessed using CLR/Aitchison ordination, the Mantel test, and Procrustes analysis. The pooled samples exhibited heterogeneous microbiota profiles at the genus level and included taxa of veterinary interest, such as Chlamydia, Avibacterium, and Gallibacterium spp. Resistome profiling revealed a broad but uneven distribution of antimicrobial resistance signals, including those associated with tetracyclines, fluoroquinolones, aminoglycosides, and beta-lactams. Taxonomic and resistome profiles showed preliminary alignment at the matrix level, indicating that resistome variations are partially linked to microbial community structure.},
}

@article {pmid42655052,
year = {2026},
author = {Dai, Q and Wang, Y and Jin, M and Wang, S and Han, M},
title = {Interaction Mechanisms Among Soil Environmental Factors, Microbial Communities, and Nitrogen-Cycling Functional Genes in Cool-Climate Maize Fields.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081705},
pmid = {42655052},
issn = {2076-2607},
support = {No. YDZJ202501ZYTS403//Jilin Province Science and Technology Department/ ; },
abstract = {Cool-climate maize fields are characterized by low soil temperatures, strong seasonal hydrothermal fluctuations, and peat-influenced soil profiles, which may lead to patterns of nitrogen (N) cycling distinct from those in conventional agricultural soils. During maize growth, soils from three depths were characterized using physicochemical measurements, N-transformation and enzyme-activity assays, metagenomic sequencing, Mantel tests, variation partitioning analysis, and partial least squares path modeling (PLS-PM). Soil environmental factors varied significantly over time and with depth; soil organic matter (SOM) and total nitrogen (TN) increased with depth, while ammonium nitrogen (NH4[+]-N) predominated early and nitrate nitrogen (NO3[-]-N) predominated during the middle and late growth stages. The nitrogen fixation rate (NFR), nitrification rate (NitR), and denitrification rate (DNR) all peaked in August and showed a spatial pattern characterized by nitrogen fixation in the deepest layer and denitrification in the upper and middle layers. Bacterial communities varied less spatiotemporally than fungal communities. The genes nifK, hao, nirS/nirK, NR, nrfC, and hzsA/hzsC were identified as key nitrogen-cycling functional genes. Mantel tests and PLS-PM further characterized these relationships, with PLS-PM showing that soil physicochemical properties were positively associated with bacterial community composition (β = 0.87, p < 0.01), which, in turn, was negatively associated with N-cycling functional genes (β = -0.97, p < 0.001). Together, these pathways were associated with variation in N-cycling processes. Overall, this study advances an integrated understanding of N-cycling patterns and their potential controls in cool-climate maize fields and provides a scientific basis for optimizing N management strategies.},
}

@article {pmid42655058,
year = {2026},
author = {Pan, Y and Wang, H and Sun, L and Huang, H and Liang, W and Liu, H},
title = {Dominant Effect of Ecological Restoration on Microbial Carbon Cycle in Plant Rhizosphere of Mining Areas.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081713},
pmid = {42655058},
issn = {2076-2607},
support = {2024B03017//Key Research and Development Project of Xinjiang Uygur Autonomous Region/ ; 2024TSYCCX0017//Xinjiang Uygur Autonomous Region 'Tianshan Talent Training Program'/ ; },
abstract = {Rhizosphere microorganisms play critical roles in biogeochemical processes including carbon cycling; however, their linkages to carbon-cycling functions under distinct mine restoration approaches remain unclear. In this study, we compared natural and artificial vegetation restoration via metagenomic sequencing to characterize rhizosphere microbial communities and carbon-cycling functional genes. Artificial restoration (AR) decreased soil electrical conductivity (EC) and salt content (SC) while increasing total phosphorus and available phosphorus by 12.33% and 16.44%, respectively. AR also elevated the relative abundances of genes responsible for degrading aromatic compounds, lignin and starch, along with genes participating in carbon-fixation pathways. Taxa of the Actinomycetia, Chloroflexi, and Solirubrobacterales served as the primary contributors to genes encoding 2-isopropylmalate synthase, α-glucosidase, malate synthase, and α-mannosidase, as well as carbon-fixation-related genes, including aconitate hydratase (ACO), methylmalonyl-CoA mutase subunit (E5.4.99.2A), pyruvate orthophosphate dikinase (ppdK), and phosphoenolpyruvate carboxylase (ppc). Moreover, the relative abundances of carbon-fixation genes exhibited significant positive correlations with EC, SC, nitrate nitrogen (NO3[-]-N) and ammonium nitrogen (NH4[+]-N). Overall, microorganisms in AR soils hold relatively high genetic potential for carbon sequestration and decomposition. Such rhizosphere carbon-cycling functions are jointly shaped by restoration strategies and vegetation community composition, and our findings offer key theoretical support for mine ecological restoration.},
}

@article {pmid42655093,
year = {2026},
author = {Pu, J and Cheng, P and Guo, Y and Xiao, D and Zhang, H and Jin, D},
title = {Vagococcus changpingensis sp. nov., a Fly-Associated Bacterium with Human Gut Metagenomic Representatives: Genomic and Metagenomic Insights into Its Ecological Distribution.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081748},
pmid = {42655093},
issn = {2076-2607},
support = {2025ZD01901104 and 2025ZD01900110//National Science and Technology Major Project of China for the Prevention and Control of Emerging and Major Infectious Diseases/ ; },
abstract = {The genus Vagococcus comprises Gram-positive bacteria with a broad ecological distribution, yet its diversity and potential links between animal and human habitats remain underexplored. Here, we report two novel fly-associated strains, CY52-2[T] and CY62-2, isolated from a retail market in Beijing, China. Polyphasic taxonomic analyses demonstrated that they represent a novel species, for which we propose the name Vagococcus changpingensis sp. nov. Large-scale mining of 805 public metagenomes identified two human gut-derived genomes that share > 99.3% ANI with V. changpingensis, extending the known distribution of this species from insects to the human gastrointestinal tract at the genomic level. Pangenome analysis revealed an open pangenome and uncovered niche-specific gene sets. These findings highlight the power of targeted metagenomics to reveal the potential ecological breadth of newly described species and provide a genomic framework for future investigations of the genus Vagococcus.},
}

@article {pmid42655130,
year = {2026},
author = {Rahman, MH and Jeon, H and Kim, H and Lee, S},
title = {Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081786},
pmid = {42655130},
issn = {2076-2607},
support = {2025//Pukyong National University/ ; Global Partnership Exchange and Capacity Building for Overseas Fisheries" program//Ministry of Oceans and Fisheries/ ; },
abstract = {Precision nutrigenomics requires a diet-microbiome-host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience.},
}

@article {pmid42655191,
year = {2026},
author = {Zhang, J and Du, X and Tang, J and Dong, X and Guo, X and Li, M and Xu, D},
title = {ESM2-Guided Context-Aware Annotation Completion Supplements Carbohydrate Metabolism Coverage in Silage Microbial Metagenomes.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081848},
pmid = {42655191},
issn = {2076-2607},
support = {31920240123//Northwest Minzu University/ ; 2024B-034//Gansu Education Department/ ; 00400-Z2200603//Northwest Minzu University/ ; 31920260001‑091//Northwest Minzu University/ ; },
abstract = {Functional annotation gaps limit the interpretation of carbohydrate metabolism in silage microbiomes. We developed Context-Aware Annotation Completion (CAAC), a framework integrating ESM2 embeddings, genomic-neighborhood features, three-class classification, confidence-tiered neighbor voting, and Enzyme Commission (EC)-to-KEGG Orthology (KO) mapping. CAAC was applied to 21 metagenomes from uninoculated and Lacticaseibacillus paracasei-inoculated silages sampled before ensiling and at 7 and 90 days. Five-fold cross-validation yielded an F1-macro of 84.64% for negative, positive, and hard-sequence classification. Among 800,000 selected annotation-poor sequences, 545,671 Tier 1 or Tier 2 predictions passed the annotation-validity and EC-to-KO mapping criteria, of which 524,814 were eligible for sample-level annotation supplementation. After silage-focused filtering and KO-EC summarization, these predictions yielded 102 KO-EC features repeatedly detected across the silage metagenomes and increased coverage in 25 of 47 carbohydrate-metabolism pathways, mainly by recovering enzyme-level components related to starch and sucrose, cellulose and cellobiose, xylan and hemicellulose, and pectin and glucuronate metabolism. Taxon-linked analyses further revealed treatment- and stage-associated patterns in the taxonomic sources of the supplemented annotations. A database-derived temporal benchmark using the July 2025 CAZy release showed 94.94% Tier 1 family-level annotation-transfer consistency. CAAC extends the enzyme-level interpretation of under-annotated silage metagenomes, while the inferred assignments remain computational predictions requiring experimental validation.},
}

@article {pmid42655208,
year = {2026},
author = {Zhu, FC and Yang, YB and Liu, PP and Liu, X and Yin, QJ and Chen, XY and Yu, S},
title = {Hepatincolaceae (Alphaproteobacteria) Symbionts of Snapping Shrimp Alpheus brevicristatus: Genomic Capacity for Functions Beyond Nutrient Scavenging.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/microorganisms14081864},
pmid = {42655208},
issn = {2076-2607},
support = {2023FY100804//Science & Technology Fundamental Resources Investigation Program/ ; 2024GXNSFBA010359//Guangxi Natural Science Foundation/ ; GUIKE AD2401006//Guangxi Science and Technology Base & Talents Fund/ ; 2023GXNSFAA026466//Guangxi Natural Science Foundation/ ; },
abstract = {Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb in size) were recovered from the gut of the snapping shrimp Alpheus brevicristatus via metagenomic sequencing. Phylogenetic and whole-genome similarity analyses confirm that these two MAGs represent two novel, undescribed genera within the family Ca. Hepatincolaceae. Metabolic reconstruction reveals that they not only retain the canonical nutrient-scavenging pathways conserved across all Hepatincolaceae members, but also encode previously undocumented functional modules for antioxidant defense, vitamin B1 and B2 biosynthesis, and short-chain fatty acid production. They maintain a high oxygen-affinity cytochrome bd terminal oxidase to thrive in the anoxic gut microenvironment. Consistent with their symbiotic lifestyle, their genomes exhibit typical signatures of reductive evolution, such as reduced genome size, low GC content, and gene loss in amino acid and nucleotide de novo biosynthesis pathways. This study presents the first reported high-quality genomes of marine Ca. Hepatincolaceae symbionts, which are predicted to possess multiple metabolic functions extending beyond nutritional mutualism.},
}

@article {pmid42655631,
year = {2026},
author = {Lai, C and Shan, F and Song, D and Chen, M and He, M and Chen, Z and Lee, X},
title = {Cross-Species Spillover of Tiger Frog Virus Caused Lethal Systemic Disease in Captive Geochelone sulcata: Etiology, Pathology, and Genomic Characterization.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080810},
pmid = {42655631},
issn = {1999-4915},
mesh = {Animals ; *Ranavirus/genetics/classification/isolation & purification/pathogenicity ; Phylogeny ; *DNA Virus Infections/veterinary/virology/pathology/mortality ; *Turtles/virology ; Genome, Viral ; China/epidemiology ; Animals, Zoo/virology ; Capsid Proteins/genetics ; Disease Outbreaks ; Metagenomics ; Genomics ; Microscopy, Electron, Transmission ; },
abstract = {In 2025, a severe mass mortality outbreak struck captive Geochelone sulcata at a zoo in Guangdong Province, China. To trace the causative agent, identify the viral strain and characterize associated pathological lesions, respiratory tract samples collected from diseased tortoises were subjected to a combined technical workflow. Metagenomic high-throughput sequencing was first applied to screen for potential pathogens, followed by virus isolation via cell culture. Transmission electron microscopy (TEM) was used to observe viral morphology. The major capsid protein (MCP) gene was amplified by PCR for molecular identification, and whole-genome sequencing together with phylogenetic analysis was performed to clarify the genetic features of the isolate. The results verified that ranavirus was the primary pathogen responsible for the mortality. Pathological examination demonstrated acute necrosis, hemorrhage and inflammatory infiltration in multiple organs including the liver, spleen, lung, and pancreas. TEM observation revealed typical iridovirus-like particles with an average diameter of approximately 70 nm. Molecular and genomic analyses confirmed the pathogen as Tiger Frog Virus (TFV) of the genus Ranavirus, designated TFV-CN2025, which shared 99.8% nucleotide sequence homology with known TFV reference strains. To our knowledge, this is the first report of lethal TFV infection in G. sulcata, which provides detailed pathological evidence for this cross-species transmission event from amphibian hosts to terrestrial chelonians. Our findings indicate that TFV poses considerable risks to the tortoise breeding industry and ecological security in China. We therefore suggest incorporating TFV detection into routine quarantine and disease surveillance programs for captive tortoises.},
}

Animals
*Ranavirus/genetics/classification/isolation & purification/pathogenicity
Phylogeny
*DNA Virus Infections/veterinary/virology/pathology/mortality
*Turtles/virology
Genome, Viral
China/epidemiology
Animals, Zoo/virology
Capsid Proteins/genetics
Disease Outbreaks
Metagenomics
Genomics
Microscopy, Electron, Transmission

@article {pmid42655634,
year = {2026},
author = {La Vignera, S and Condorelli, RA},
title = {Non-Sexual Transmission of Papillomavirus: Is It Part of Our Virome?.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080812},
pmid = {42655634},
issn = {1999-4915},
mesh = {Humans ; *Papillomavirus Infections/transmission/virology/epidemiology ; Female ; *Human Papillomavirus Viruses/genetics/classification/physiology ; Infectious Disease Transmission, Vertical ; *Virome ; Infant, Newborn ; Pregnancy ; Fomites/virology ; Prevalence ; *Papillomaviridae/genetics ; Milk, Human/virology ; Infant ; },
abstract = {BACKGROUND: Human papillomavirus (HPV) has traditionally been considered a sexually transmitted infection, yet accumulating evidence demonstrates that HPV can be acquired through multiple non-sexual routes. Understanding these alternative transmission pathways is critical for interpreting HPV detection in non-sexually active populations and for refining public health strategies.

METHODS: This review synthesizes current evidence on non-sexual HPV transmission routes, including vertical (transplacental, intrapartum), perinatal oropharyngeal colonization, fomite contamination, breast milk transmission, and horizontal non-sexual contact. We examine HPV prevalence data from female virgins, neonates, infants, and children, and evaluate metagenomic evidence positioning HPV as a component of the human virome across multiple body sites.

RESULTS: Published studies report that vertical transmission occurs in approximately 18.2% of HPV-positive mothers, with neonatal HPV positivity of 3.4% at birth and 100% genotype concordance in transmission pairs. Transplacental transmission has been documented in 10.2% of concordant mother-placenta-newborn triads. Reviewed studies report oropharyngeal colonization at birth reaching 58.2% following vaginal delivery, with 94.3% of colonized neonates clearing infection by 24 months. HPV DNA has been detected on fomites and medical devices, in breast milk (8.6-15%), and across body sites in healthy adults (skin 61.3%, vagina 41.5%, oral cavity 30%, gut 17.3%). Metagenomic studies identify HPV DNA in 68.9% of healthy individuals, with 109 distinct types detected. Female virgins show HPV prevalence ranging from 0-51.1% across studies.

CONCLUSIONS: The reviewed evidence suggests that HPV exhibits characteristics of a ubiquitous virome component with multiple non-sexual acquisition routes. These findings have important implications for vaccination strategies, screening interpretation, infection control in healthcare settings, and counseling of pediatric cases and non-sexually active individuals.},
}

Humans
*Papillomavirus Infections/transmission/virology/epidemiology
Female
*Human Papillomavirus Viruses/genetics/classification/physiology
Infectious Disease Transmission, Vertical
*Virome
Infant, Newborn
Pregnancy
Fomites/virology
Prevalence
*Papillomaviridae/genetics
Milk, Human/virology
Infant

@article {pmid42655644,
year = {2026},
author = {Amoia, SS and Giampetruzzi, A and Neto, FFS and António, LF and Pais da Cunha, AT and Minafra, A},
title = {Plant Viral Metagenomic Analysis from a Preliminary Field Survey in Angola Reveals Complex Mixed Infections in Vegetable Crops.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080822},
pmid = {42655644},
issn = {1999-4915},
support = {EuropeAid/171171/DD/ACT/Multi (FOOD/2021/429-168)//European Union/ ; },
mesh = {*Metagenomics ; *Plant Viruses/genetics/classification/isolation & purification ; Angola ; *Plant Diseases/virology ; *Crops, Agricultural/virology ; *Vegetables/virology ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Coinfection/virology ; },
abstract = {Climatic changes are heavily affecting the sustainability of vegetable crops crucial for food supply worldwide, mainly in subtropical countries. One of the main threats to food security is the spread of diseases caused by plant viruses, favored by irregular rains and extreme temperatures, which reduce crop yield and quality. During a preliminary field survey carried out in two provinces of Angola in 2024, a few symptomatic plants of tomato, habanero pepper, common bean and a wild weed were sampled. These plants generally showed dwarfing, yellowing and leaf curl and were submitted to high-throughput sequencing to detect any viral agent. The evidence of mixed infections of several polyphagous viruses with RNA or DNA genomes, variously affecting the selected plants, was assessed from the sequence analysis and further confirmed for most samples by molecular tests, like (RT)-PCR or qPCR. Emerging polero-, begomo and tobamoviruses were denoted as infecting these plants. A novel, previously unknown carlavirus was also described in a wild weed. Most of those viruses are efficiently mechanically transmitted or airborne vehiculated by insect vectors. Although based on a limited number of samples, this study provides a first insight into the diversity of viruses infecting vegetable crops in Angola. It also highlights the pressing need for a broader monitoring to better understand virus distribution and epidemiology, and suggests the use of virus-free seeds to reduce the potential risk to crop production.},
}

*Metagenomics
*Plant Viruses/genetics/classification/isolation & purification
Angola
*Plant Diseases/virology
*Crops, Agricultural/virology
*Vegetables/virology
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
*Coinfection/virology

@article {pmid42655670,
year = {2026},
author = {Cullinane, A and Garvey, M and Collins, D and Lyons, R and Nelly, M and Grimes, A},
title = {Equine Ulcerative Genital Lesions Associated with Parapoxvirus.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080852},
pmid = {42655670},
issn = {1999-4915},
mesh = {Animals ; Horses ; *Horse Diseases/virology/epidemiology/pathology ; Phylogeny ; Female ; *Poxviridae Infections/veterinary/virology/epidemiology/pathology ; *Parapoxvirus/genetics/classification/isolation & purification ; Disease Outbreaks/veterinary ; Male ; DNA, Viral/genetics ; Ireland/epidemiology ; Penis/virology/pathology ; *Ulcer/veterinary/virology ; },
abstract = {In 2026, a widespread outbreak of ulcerative dermatitis of unknown aetiology occurred in breeding horses in Ireland. The lesions resembled those associated with equine herpesvirus 3 (EHV3) infection, i.e., papules, vesicles, and ulcers on the penis of stallions and on the vulval and anal areas of mares. This study aimed to identify the probable causative agent. The methods applied included metagenomic sequencing of DNA, phylogenetic analysis, and real-time PCR. Metagenomic analysis directly from a penile sample confirmed the presence of equine parapoxvirus (EqPPV) DNA. Phylogenetic analysis indicated that it clustered closely with EqPPV first identified in Finland in 2013 from a horse with proliferative dermatitis, and associated with outbreaks of pastern dermatitis in trotting racehorses in 2021/2022. Comparison of the amino acid sequences of the DNA polymerase gene showed that the EqPPVs from Finland and Ireland share 99% identity in contrast to 76-80% with other members of the parapoxvirus genus. A specific PCR test for EqPPV, adapted from that developed in Finland, successfully identified viral DNA in samples from 22 of 25 suspect cases that tested negative for EHV3. In conclusion, this study is the first documented outbreak of genital lesions in breeding horses associated with EqPPV.},
}

Animals
Horses
*Horse Diseases/virology/epidemiology/pathology
Phylogeny
Female
*Poxviridae Infections/veterinary/virology/epidemiology/pathology
*Parapoxvirus/genetics/classification/isolation & purification
Disease Outbreaks/veterinary
Male
DNA, Viral/genetics
Ireland/epidemiology
Penis/virology/pathology
*Ulcer/veterinary/virology

@article {pmid42655678,
year = {2026},
author = {Lapshina, VK and Gorbacheva, AA and Nikolaeva, PA and Grigoryan, DA and Stetsenko, IF and Luong, MT and Tran, TV and Yuzefovich, AP and Prikhodko, IO and Alekseev, AY and Yudin, SM and Shipulin, GA and Matsvay, AD and Skvortsova, VI},
title = {Bat-Associated Parvoviruses: High Genetic Diversity and Novel Viruses in Gia Lai and Dong Nai Provinces, Vietnam.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080860},
pmid = {42655678},
issn = {1999-4915},
support = {Ecolan M-1.7//Joint Vietnam-Russia Tropical Science and Technology Research Center/ ; 124021900144-4//Federal Medical-Biological Agency/ ; },
mesh = {Animals ; *Chiroptera/virology ; Vietnam/epidemiology ; *Genetic Variation ; Phylogeny ; *Parvovirus/genetics/classification/isolation & purification ; *Parvoviridae Infections/veterinary/virology/epidemiology ; },
abstract = {Bats are recognized as key reservoirs for diverse viruses, including members of the Parvoviridae family. Vietnam hosts an exceptionally wide variety of bat species, yet the diversity of parvoviruses in these populations remains largely unexplored. This study provides the first survey of parvoviruses in bats from Gia Lai and Dong Nai provinces, screening 150 samples from 26 bat species and detecting parvoviruses in 38 (25%). A total of 45 viral operational taxonomic units (OTUs) were identified, encompassing four parvoviral subfamilies: Parvovirinae, Densovirinae, Penbrevirinae, and Hamavirinae. However, only two of these OTUs were attributed to ICTV-accepted species. Twenty-six OTUs were assigned to recognized genera but exhibited insufficient sequence similarity to established species, suggesting they may represent novel species within these genera. The remaining 25 OTUs could not be assigned to any ICTV-accepted genus, including 14 that remained unclassified even at the subfamily level, indicating the presence of novel parvovirus lineages at the genus rank or above. Overall, 95% of detected viral variants were classified as potentially novel, revealing a substantial reservoir of Parvoviridae diversity in the region. Phylogenetic analysis of vertebrate-infecting parvoviruses showed that the detected dependoparvoviruses were most closely related to viruses from primates and pinnipeds, while the chaphamavirus sequences formed a clade associated with carnivore viruses, and the embehamavirus sequences showed high homology to a virus previously detected in human plasma from a neuroinfection case. These results underscore the importance of comprehensive bat virome surveillance and enhance our understanding of the viral diversity and potential zoonotic threats posed by parvoviruses.},
}

Animals
*Chiroptera/virology
Vietnam/epidemiology
*Genetic Variation
Phylogeny
*Parvovirus/genetics/classification/isolation & purification
*Parvoviridae Infections/veterinary/virology/epidemiology

@article {pmid42655684,
year = {2026},
author = {Roberts, H and Waite, DW and Khan, S and Veerakone, S and Tang, J and Thompson, JR},
title = {Development and Validation of a Passive Surveillance System for Early Detection of Pepino Mosaic Virus in Commercial Greenhouse Facilities.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/v18080866},
pmid = {42655684},
issn = {1999-4915},
support = {407136//Ministry for Primary Industries/ ; },
mesh = {*Plant Diseases/virology ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; *Environmental Monitoring/methods ; Water Microbiology ; },
abstract = {The use of environmental nucleic acid (eNA), both DNA and RNA, as a means for surveillance has been a fixture in the scientific literature for many years. The application of environmental screening for genomic signatures of organisms of interest-particularly those of diagnostic concern-is a promising yet still under-utilised tool for sample screening. While the literature tends to focus on the use of high-throughput sequencing (HTS) to detect organisms of interest using metagenomic or metatranscriptomic sampling, this approach is not cost-competitive with more traditional targeted molecular test methods. Consequently, eNA sampling still has not gained significant traction in practical settings despite its popularity in ecological research. To address these issues in a biosecurity context, we report here the development of a testing protocol to monitor irrigation water for the presence of pepino mosaic virus (PepMV) that also includes an endogenous Sphingomonas control. We employed passive sampling through the immersion of filtering devices into the water system at three commercial growing operations at two time points to collect samples with minimal hands-on effort, while simultaneously developing and validating molecular methods for the recovery of RNA competent for both PCR and high-throughput sequencing. We demonstrate not only the ability to detect PepMV from water collections, but also that the method is robust to the accumulation of non-target material and does not lose signal if viruses are only transiently present in the water system. Finally, we developed a capsid-integrity pre-treatment protocol for differentiating between intact and denatured (non-viable) virus particles during PCR testing. This work presents a low-cost and low-effort technique for proactive screening of commercial greenhouse facilities to facilitate early detection of harmful crop pests and pathogens.},
}

*Plant Diseases/virology
High-Throughput Nucleotide Sequencing
RNA, Viral/genetics
*Environmental Monitoring/methods
Water Microbiology

@article {pmid42655786,
year = {2026},
author = {Ashfaq, MS and Tharwat, M and Ahmed, S and Shaukat, A and Nassar, N and Abid, S and Abid, MA and Alshanbari, FA},
title = {Microbiome Engineering in Dairy Cattle: A Critical Review of Strategies for Disease Resistance, Productivity, and Sustainable Farming.},
journal = {Veterinary sciences},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/vetsci13080766},
pmid = {42655786},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {Dairy production currently faces three converging challenges: the escalation of antimicrobial resistance (AMR), rising global food demand, and stricter regulatory requirements for reducing enteric methane emissions. This review evaluates probiotics, prebiotics, fecal microbiota transplantation (FMT), metagenomic tools, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based synthetic biology for dairy cow microbiome engineering, applying a Technology Readiness Level (TRL) 1-9 framework to assess the translational maturity of each strategy. The quantitative ranges below are from individual controlled or field studies unless indicated otherwise, and they represent the variation from study to study in different breeds, feeds, and stages of lactation, as well as in management systems. A systematic literature search was conducted across five major databases for the period 2020-2026. Applying the TRL framework revealed that conventional probiotics have reached field-ready maturity (TRL 7-8), boosting milk yield by 0.5-1.5 kg/d and lowering somatic cell counts by 20-40%. Calf gut maturation was found to be two to three weeks faster when FMT was used (TRL 5-6). Controlled conditions (TRL 2-3) showed a 10-20% reduction in methane emissions using engineered rumen bacteria (CRISPR). Intervention failures primarily stem from host-microbiome misalignment rather than microbial product design. The key translational gap is shifting from uniform herd-level to precision-guided individualized dosing. Standardized data infrastructure, regulatory frameworks for engineered biologics, and integration with precision livestock farming platforms are required to reduce antibiotic use and lower methane emissions within a One Health framework.},
}

@article {pmid42655905,
year = {2026},
author = {Yi, H and Jiang, A and Jiao, D and Cao, X and Zhou, Y and Song, C},
title = {Innovatively Unlocking Anammox Driven by Nitrite Accumulation in a nrfA-Deficient Shewanella oneidensis MR-1 Consortium.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {8},
pages = {e70526},
doi = {10.1002/wer.70526},
pmid = {42655905},
issn = {1554-7531},
mesh = {*Shewanella/metabolism/genetics ; *Nitrites/metabolism ; *Bacterial Proteins/genetics/metabolism ; Nitrogen/metabolism ; Bioreactors/microbiology ; },
abstract = {With the advancement of industrialization and urbanization, nitrogen pollution has become increasingly severe, and accelerating the nitrogen cycle is of great significance for nitrogen removal in wastewater treatment. To enhance the nitrogen (N) removal efficiency, we constructed a novel coupled system integrating anammox with Shewanella oneidensis MR-1. We specifically focused on the functional differences between its wild-type and a nrfA-deficient mutant (ΔnrfA). We systematically evaluated the N removal performance, microbial community structure, and nitrogen/carbon metabolic functional genes under different inoculation ratios. Although the wild-type strain could supply nitrite (NO2 [-]-N) for anammox via dissimilatory nitrate reduction to ammonium (DNRA), its excessive inoculation triggered substrate competition with denitrification, weakening the anammox dominance. Conversely, the mutant strain can cause the accumulation of NO2 [-]-N by blocking the DNRA pathway, thereby forming a stable synergistic interaction with anammox bacteria. The coupled system achieved a maximum total N removal efficiency of 97% with the fastest reaction kinetics at an optimal anammox-to-mutant volume ratio of 5:1. Metagenomic analysis corroborated these findings, revealing significant enrichment of key anammox functional genes (hzs and hdh) under this optimized condition. In summary, strategically coupling anammox with an electron-transfer-capable, DNRA-deficient mutant ensures a sustained NO2 [-]-N supply. This genetic manipulation strategy offers a novel, efficient, and stable paradigm for advancing anaerobic nitrogen removal in nitrate-laden wastewater treatment.},
}

*Shewanella/metabolism/genetics
*Nitrites/metabolism
*Bacterial Proteins/genetics/metabolism
Nitrogen/metabolism
Bioreactors/microbiology

@article {pmid42656127,
year = {2026},
author = {Kim, D and Lee, S and Kang, DY and Park, BY and Oh, EH and Kang, J and Choi, MH and Yoon, JG and Jeong, SH},
title = {Development and Validation of Mock Communities as Quality Control Materials for Clinical Metagenomic Next-Generation Sequencing.},
journal = {Annals of laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.3343/alm.2026.0143},
pmid = {42656127},
issn = {2234-3814},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (NGS) enables comprehensive detection of a broad spectrum of microorganisms. However, its clinical application faces two major challenges: the development of appropriate microbiome-based biomarkers and the need to ensure the reproducibility and quality of the microbiome analytical workflow. Therefore, we developed four types of bead-based mock communities as standard materials for microbiome analysis and evaluated potential experimental biases arising from nucleic acid extraction and sequence analysis.

METHODS: Mock communities were assembled from strains isolated from clinical specimens and selected considering Gram reaction, taxonomic phylogeny, and prevalence, and processed into frozen beads. The communities were analyzed using shotgun whole-metagenome sequencing. The effect of DNA extraction kit choice was evaluated using the Thermo Fisher Scientific MagMAX Microbiome Ultra Nucleic Acid Isolation Kit and Qiagen PowerSoil Kit.

RESULTS: Four types of mock communities comprising 26 species commonly found in the gastrointestinal tract, respiratory tract, skin, and genital tract plus cerebrospinal fluid were developed considering Gram reaction, GC content, and phylogenetic distribution. Across 25 repeated analyses, the median repeatability of each taxon was 18.97% (range, 2.87%-107.38%), while within-laboratory imprecision was 26.22% (range, 9.26%-153.83%). Repeatability remained below 10% for most dominant taxa with relative abundances >20%. The choice of DNA extraction kit had a significant effect on taxonomic distributions.

CONCLUSIONS: Microbial mock communities are essential QC materials for clinical metagenomic NGS. Further studies are needed to minimize variability and establish a standardized protocol for clinical implementation.},
}

@article {pmid42656568,
year = {2026},
author = {Sufi, F},
title = {Agentic AI for trustworthy synthetic microbial genomics: a perspective on generation, validation, and governance.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1903746},
pmid = {42656568},
issn = {2673-7647},
abstract = {Synthetic microbial genomic data are becoming increasingly important for benchmarking microbial genome analysis pipelines, simulating rare taxa, evaluating metagenomic workflows, and supporting reproducible computational biology. Recent genomic foundation models demonstrate that biological sequences can be modelled at unprecedented scale, with emerging capacity for genome-level interpretation, generation, and design. However, the scientific value of synthetic microbial genomic data depends not only on whether sequences can be generated, but whether they are biologically plausible, computationally useful, reproducible, and responsibly governed. This Perspective argues that agentic AI can provide the missing orchestration layer for trustworthy synthetic microbial genomics. Rather than treating synthetic data generation as a single model output, agentic workflows can coordinate specialised roles for sequence generation, biological plausibility assessment, taxonomic validation, functional annotation, contamination detection, downstream benchmarking, provenance logging, and governance review. I propose a validation-first agentic framework in which synthetic microbial genomes, plasmids, phages, and metagenomic profiles are iteratively generated, evaluated, revised, and documented before release or downstream use. Such a framework can help transform synthetic microbial genomic data from computational artefacts into auditable scientific infrastructure with explicit validation gates, escalation criteria, and machine-readable provenance.},
}

@article {pmid42656597,
year = {2026},
author = {Pabon-Rodriguez, FM and Ayodo, G},
title = {Using nanopore metagenomics to characterize pathogens in febrile patients from a highland of Western Kenya.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1884846},
pmid = {42656597},
issn = {2235-2988},
mesh = {Humans ; Kenya/epidemiology ; *Metagenomics/methods ; Female ; Male ; *Fever/microbiology/etiology ; Malaria/epidemiology/diagnosis ; Adult ; High-Throughput Nucleotide Sequencing ; *Nanopore Sequencing/methods ; Bacteria/genetics/classification/isolation & purification ; Child, Preschool ; Adolescent ; Young Adult ; Child ; Middle Aged ; },
abstract = {INTRODUCTION: Febrile illness remains a leading cause of morbidity in sub-Saharan Africa despite substantial reductions in malaria transmission. As malaria positive cases decrease, an increasing number of patients with febrile illnesses test negative for Plasmodium infection, leaving their causes unresolved. As a result of the diagnostic gap, patients receive presumptive antimalarial treatment, unnecessary antibiotics and experience delayed therapy.

METHODS: We conducted a nanopore metagenomic next-generation sequencing (mNGS) investigation of 168 archived blood samples collected from febrile patients in Kipsamoite and Kapsisywa sites in Nandi County, a highland region in western Kenya experiencing declining malaria transmission, between 2012 and 2020. The study used exploratory taxonomic profiling to identify microbial DNA/RNA signatures in archived plasma samples and described organisms with known or potential clinical relevance, while classifying detected organisms into common commensal, skin-associated, and environmental taxa. Demographic and clinical data linked to samples were used to fit multivariable logistic regression models to assess associations.

RESULTS: Sequencing revealed substantial microbial heterogeneity, including frequent detection of common skin/environmental taxa, opportunistic organisms, ubiquitous viruses, and a smaller number of organisms with established fever-causing potential. The detections are interpreted as molecular evidence of microbial nucleic acid, not as proof of active infection or fever causality. Malaria-positive subjects had a higher mean number of identified pathogens compared to malaria-negative subjects (3.78 vs. 2.14; p = 0.002), despite a baseline microbial landscape dominated by commensal flora, environmental organisms, and ubiquitous viruses.

DISCUSSION: Nanopore mNGS is a viable tool for identifying non-malarial febrile pathogens in western Kenya. Future efforts must combine systematic sampling with field-deployable contamination controls and causal confirmation frameworks to optimize regional antimicrobial stewardship and surveillance.},
}

Humans
Kenya/epidemiology
*Metagenomics/methods
Female
Male
*Fever/microbiology/etiology
Malaria/epidemiology/diagnosis
Adult
High-Throughput Nucleotide Sequencing
*Nanopore Sequencing/methods
Bacteria/genetics/classification/isolation & purification
Child, Preschool
Adolescent
Young Adult
Child
Middle Aged

@article {pmid42656796,
year = {2026},
author = {Keller, JT and Lim, SJ and Natarajan, O and Cropper, N and Dishaw, LJ and Breitbart, M},
title = {Draft genome sequence of Dermacoccus nishinomiyaensis Y5.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42656796},
issn = {2578-9430},
abstract = {We report the draft genome sequence of Dermacoccus nishinomiyaensis Y5 isolated from a glycerol stock prepared from a fungal culture from the gill of the lucinid bivalve, Stewartia floridana . This bacterial strain is gram-positive, coccus-shaped, and citrate-positive. Its draft genome of 3.3 Mb was assembled with 100% completeness, comprising 11 contigs and 2,937 protein-coding genes. Dermacoccus nishinomiyaensis Y5 shared 98.9% average nucleotide identity (ANI) with its closest genome relative, D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome. Further investigation is needed to identify the source and pathogenicity of D. nishinomiyaensis Y5.},
}

@article {pmid42657129,
year = {2026},
author = {Xiao, H and Rao, YX and Xu, ML and Wang, W and Li, CQ},
title = {Pulmonary Infiltrates, Airway Mucosal Lesions and Respiratory Microbiology After Freshwater Drowning: A Case Report.},
journal = {Respirology case reports},
volume = {14},
number = {8},
pages = {e70731},
pmid = {42657129},
issn = {2051-3380},
abstract = {Early pulmonary abnormalities after freshwater drowning can be overinterpreted as bacterial pneumonia, especially when inflammatory biomarkers and respiratory microbiology are positive. A 20-year-old man was resuscitated after approximately 2 min of freshwater submersion. Day 1 chest CT showed bilateral lower-lobe-predominant opacities compatible with non-cardiogenic pulmonary oedema and aspiration-related lung injury, with near-complete resolution by Day 25. Day 3 bronchoscopy showed diffuse, non-removable, millet-seed-like whitish tracheal mucosal protrusions with hyperaemia and oedema, compatible with acute irritative airway injury. BALF mNGS detected multiple gram-negative bacterial signals, predominantly Klebsiella pneumoniae, while sputum culture yielded ESBL-negative, susceptible K. pneumoniae. Possible drowning-associated pneumonia was considered because of aspiration, fever, markedly elevated inflammatory biomarkers and concordant microbiology; however, rapid radiological improvement and clinical stability suggested a substantial non-infectious component. The patient recovered after an 8-day course of piperacillin-tazobactam without antibiotic escalation, corticosteroids, mechanical ventilation or acute respiratory distress syndrome.},
}

@article {pmid42657421,
year = {2026},
author = {Su, R and Chan, PT and Zhang, X and Chen, J and Lee, S and Yang, X and Chan, HY and Lin, Y and Li, J and Yan, Q and Liu, H and He, Z},
title = {Seagrass-derived carbon suppresses nitrification and N2O emissions by Comammox and canonical nitrifier communities.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag220},
pmid = {42657421},
issn = {2730-6151},
abstract = {Seagrass meadows are critical regulators of coastal biogeochemical cycling, particularly through the exudation and accumulation of organic carbon that enriches their rhizosphere far beyond ambient marine levels. Microbially driven nitrification is a key process controlling nitrous oxide (N2O) emissions, yet the ecological roles of complete ammonia oxidizers (Comammox) and canonical nitrifiers in seagrass ecosystems are poorly understood. Here, seagrass sediments (SS) exhibited significantly (P < .05) lower nitrification and N2O production rates than non-seagrass sediments, where nitrification was the dominant N2O source. We characterized Comammox for the first time in a seagrass ecosystem, revealing that they displayed potential nitrification rates lower than ammonia-oxidizing bacteria or ammonia-oxidizing archaea. Notably, Comammox showed the lowest potential N2O production rates and negative CO2 fluxes. Metagenomic profiles revealed lower relative abundances of genes associated with nitrification and N2O-producing pathways in SS, while metatranscriptomic analysis identified significant (P < .05) down-regulation of the core nitrification genes. In contrast, genes involved in sugar transport and metabolism generally showed positive transcriptional changes. This study identifies a key microbial mechanism through which seagrass-derived carbon may contribute to lower nitrification and N2O emissions, highlighting the potential of microbiome engineering in seagrass restoration and conservation for climate mitigation.},
}

@article {pmid42657436,
year = {2026},
author = {Chaux, F and Vojvoda Zeljko, T and Vuković, BB and Burns, JA and Le Perrun, T and Žižek, M and Bannerman, BP and Mason, DTB and Garrido, C and Xu, Z and Dorrell, RG and Godrijan, J},
title = {The Calcidiscus leptoporus genome reveals vitamin-mediated holobiont interactions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag222},
pmid = {42657436},
issn = {2730-6151},
abstract = {Coccolithophores are major marine phytoplankton that contribute to ocean carbon cycling through both organic carbon fixation and calcium carbonate biomineralization, yet the functional basis of their interactions with phycosphere bacteria remains poorly resolved. Here, we present the nuclear genome of the haploid phase of the coccolithophore Calcidiscus leptoporus, a coccolithophore that calcifies in both life-cycle stages. We combined host genome analysis, genome-resolved characterization of associated bacteria, and a four-month vitamin-manipulation experiment to test how B-vitamin biosynthetic complementarity relates to host performance and phycosphere community assembly. Metabolic reconstructions indicate partitioned B-vitamin biosynthtic potential: the host encodes pathways for B2, B5, B6, and B9, including a rare fused B5 biosynthesis gene, but lacks complete pathways for B1, B3, B7, and B12. These missing functions were distributed among recurrent bacterial taxa, with no single bacterial MAG encoding the full set of host-missing vitamins. Across the experiment, bacterial community composition was structured primarily by the experimental phase, while vitamin treatments secondarily influenced which taxa became enriched at later stages. Consistent with genome-inferred auxotrophy, B-vitamin availability constrained long-term growth under the tested conditions, with B1 alone providing partial rescue and vitamin-replete treatments showing equal or stronger responses. Together, these data establish C. leptoporus as a genomic model for coccolithophore biology and holobiont interactions, while providing a testable framework linking vitamin economies to phycosphere assembly and host performance.},
}

@article {pmid42641710,
year = {2026},
author = {Dropa, M and Souleymane, AA and Kisielius, V and Kilcoyne, E and Carvalho, PN and Walsh, F and Shryane, T and Lyu, T},
title = {Emerging chemical and biological contaminants fate and removal in a full-scale multi-cell integrated constructed wetland.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135723},
doi = {10.1016/j.biortech.2026.135723},
pmid = {42641710},
issn = {1873-2976},
abstract = {The stringent wastewater regulation is being expanded to include chemical micropollutants and strengthened antimicrobial resistance (AMR) surveillance, prompting the evaluation of evolving nature-based solutions for wastewater treatment. This study investigated a full-scale Integrated Constructed Wetland (ICW) in Ireland, combining chemical analysis, metagenomics, and quantitative PCR to assess pharmaceutical micropollutants, microbial community composition, and antibiotic resistance genes (ARGs) across the treatment wetland cells. A total of 67 pharmaceuticals were analysed, with 21 compounds consistently detected in water. Median concentrations decreased from 450 ng/L in the influent to 245 ng/L in the final effluent, despite a temporary increase to 710 ng/L in an intermediate cell. Compound-specific apparent removal ranged from <30% to >99%, and most compounds showed low ecological risk, although clarithromycin, lidocaine, and diclofenac exhibited risk quotient (RQ) values >1 at discharge. In sediments, micropollutant concentrations ranged from 8.7 to 36.7 ng/g dry weight, with higher concentrations observed in downstream cells and an RQ > 1 for benzotriazole. Relative ARG abundance in water decreased from 5.53 × 10[-6] to 9.62 × 10[-][8] ARGs/16S (∼2.5-log reduction), while sediment samples showed higher relative abundance (2.12 × 10[-][2] to 4.48 × 10[-][4] ARGs/16S) with an overall 1.8-log reduction. These results demonstrate that full-scale ICWs can effectively attenuate both chemical and biological contaminants while highlighting the importance of sediment-associated retention, providing important evidence to support their role in future risk-based wastewater management and nature-based solutions for wastewater treatment strategies.},
}

@article {pmid42641809,
year = {2026},
author = {Wang, J and Zhang, D and Hu, S and Guo, H and Zou, L and Wang, N and Xie, J and Wang, Z and Hao, M and Da, Y and Wang, M and Song, L and Li, H and Sun, B},
title = {Limosilactobacillus reuteri and Lactobacillus johnsonii intervention ameliorates gestational diabetes mellitus-associated sex-specific placental nutrient transporter abnormalities: Links with tryptophan metabolism and aryl hydrocarbon receptor signaling.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113510},
doi = {10.1016/j.diabres.2026.113510},
pmid = {42641809},
issn = {1872-8227},
abstract = {AIMS: Gestational diabetes mellitus (GDM) is a common pregnancy complication associated with maternal metabolic abnormalities and adverse offspring outcomes. Although GDM is closely linked to gut microbiota dysbiosis, key probiotic strains and underlying mechanisms remain unclear. This study aimed to identify potential probiotics using microbial signals from clinical GDM cases and a mouse model.

METHODS: Metagenomic sequencing was performed on fecal samples from normal and GDM pregnant women; a GDM mouse model was then established for candidate probiotic screening. Combined intervention with Limosilactobacillus reuteri and Lactobacillus johnsonii was applied to assess glucose metabolism, inflammation, intestinal barrier, placental structure, nutrient transporter expression and tryptophan metabolism.

RESULTS: Metagenomic analysis showed reduced Lactobacillaceae in GDM women, and the two strains were identified as candidates. The intervention improved glycemic control, insulin resistance, inflammation and colon barrier function, and alleviated placental lesions. Placental nutrient transporters exhibited sex-specific disorders that were normalized by probiotics. Maternal plasma 5-hydroxyindoleacetic acid (5-HIAA) was reduced in GDM mice and restored after intervention, correlating with metabolic indices, placental status, fetal growth and aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: Combined L. reuteri and L. johnsonii intervention improved GDM-associated maternal metabolic and sex-specific placental abnormalities.},
}

@article {pmid42642033,
year = {2026},
author = {Saiz-Gonzalo, G and Al-Humadi, AW and McSweeney, S and le Roux, CW and Bleiel, SB},
title = {A high-fibre snack containing Lacticaseibacillus rhamnosus GG for healthy adults: a randomised, double-blind, placebo-controlled crossover trial.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-19},
doi = {10.1163/18762891-bja00126},
pmid = {42642033},
issn = {1876-2891},
abstract = {Probiotics have gained increasing evidence for their roles in health and disease. Microencapsulation can improve the consistency and efficacy of probiotic-fortified foods by enabling safer delivery to target regions of the gastrointestinal tract. We evaluated a probiotic snack bite containing microencapsulated Lacticaseibacillus rhamnosus GG. Twenty-five healthy adults consumed one snack daily for 28 days, then a 7-day washout, followed by crossover. Outcomes included gastrointestinal health analysis, bowel movement ease and frequency, bloating, overall gut comfort, shotgun metagenomics and systemic biomarkers of barrier, brain function and inflammation. Compared with the lower-fibre control snack, the probiotic snack was associated with easier bowel movements and fewer constipation reports at end of period, while bloating remained low in both periods. However, because the products differed in nutritional composition, these findings cannot be attributed to L. rhamnosus GG alone inflammatory and barrier biomarkers did not differ between treatments and stayed within healthy ranges. In an exploratory subgroup with elevated baseline serotonin, end-of-period serotonin was lower after the probiotic-containing snack than after the control snack, whereas brain-derived neurotrophic factor was unchanged. Daily intake of microencapsulated Lacticaseibacillus rhamnosus GG was well tolerated and was associated with exploratory difference in bowel habit and serum serotonin in a subgroup, without detectable changes in systemic inflammation or barrier biomarkers.},
}

@article {pmid42642216,
year = {2026},
author = {Shirai, N and Bhosle, A and Nzabarushimana, E and Shen, J and Yan, Y and Kim, H and Upreti, C and Ananchuensook, P and Stoffel, E and Kupfer, SS and Chung, DC and Thompson, KN and Drew, DA and Stadler, ZK and Huttenhower, C and Chan, AT and Nguyen, LH},
title = {Multi-kingdom signatures of the gut microbiome in Lynch syndrome: a prospective model for colorectal cancer evolution.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339088},
pmid = {42642216},
issn = {1468-3288},
}

@article {pmid42642268,
year = {2026},
author = {Hudu, SA and Morad, EA and Alhazimi, GM and Shalaby, NM and Jimoh, AO},
title = {Microbiome-metabolome multi-omics biomarkers for infectious disease prognosis: Current evidence, AI-driven integration, and translational challenges.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.08.043},
pmid = {42642268},
issn = {0929-6646},
abstract = {Microbiome-metabolome interactions are emerging as promising predictors of infectious disease, beyond conventional pathogen detection. Growing evidence shows that microbial dysbiosis, altered microbial-derived metabolites, and host metabolic reprogramming are associated with disease severity, immune dysfunction, treatment response, and mortality across infectious diseases. High-throughput sequencing, metagenomic next-generation sequencing, and nuclear magnetic resonance platforms have identified microbial and metabolic signatures that are prognostic for inflammatory activation, oxidative stress, mitochondrial dysfunction, and immune dysregulation. Integration of microbiome and metabolomic datasets with multi-omics frameworks may improve prognostic stratification compared to single-omics approaches. Artificial intelligence and machine-learning models, such as random forests, gradient boosting, and deep learning algorithms, have demonstrated promising potential for identifying high-dimensional prognostic patterns and aiding risk prediction. However, most of the available evidence remains exploratory and is hampered by cohort heterogeneity, small sample sizes, cross-sectional study designs, batch effects, limited external validation, and difficulties with model interpretability and reproducibility. Current evidence supports the potential of microbiome-metabolome biomarkers as complementary prognostic tools rather than routine clinical diagnostics. Future progress will require large, multicenter longitudinal studies, harmonized analytical frameworks, explainable artificial intelligence models, and equitable implementation strategies to enable clinically reliable precision infectious-disease prognostics.},
}

@article {pmid42642381,
year = {2026},
author = {Birkeland, EE and Kværner, AS and Avershina, E and Bucher-Johannessen, C and Bemanian, V and Blix, HS and Hjartåker, A and de Vos, WM and Ursin, G and Hoff, G and Randel, KR and Botteri, E and Berstad, P and Rounge, TB},
title = {Microbiome signatures for detection of colorectal lesions in population-based FIT screening.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42642381},
issn = {2041-1723},
support = {190179//Kreftforeningen (Norwegian Cancer Society)/ ; 198048//Kreftforeningen (Norwegian Cancer Society)/ ; 2020056//Ministry of Health and Care Services | Helse Sør-Øst RHF (Southern and Eastern Norway Regional Health Authority)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; Female ; Feces/microbiology ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Early Detection of Cancer/methods ; Aged ; Occult Blood ; Bacteria/genetics/classification/isolation & purification ; Norway ; Metagenome ; Precancerous Conditions/diagnosis/microbiology ; Mass Screening/methods ; },
abstract = {The gut microbiome has been linked to colorectal cancer (CRC) development, with microbe-based classifiers distinguishing between CRC patients and healthy controls. However, there is a lack of studies addressing the utility of the microbiome in screening-relevant settings, including both precancers and CRC. In this Norwegian population-based study, we used fecal immunochemical test (FIT) leftovers from 1034 FIT-positive (i.e. positive for occult blood) screening participants for gut metagenome profiling using shotgun sequencing. Using comprehensive clinical, demographic, and lifestyle data, we modeled gut microbiome associations with CRC screening outcomes. Combining microbial profiles with quantitative FIT values improved detection of premalignant lesions beyond optimizing the FIT value alone, even after incorporating established CRC risk factors. Still, the FIT value maintained superior discriminative ability for CRC. We confirmed enrichment of bacteria such as Fusobacterium nucleatum and Peptostreptococcus stomatis in CRC. In contrast, other bacteria previously associated with the presence of CRC, including Hungatella hathewayi and Clostridium symbiosum, as well as pks-negative Escherichia coli, were enriched in those with no neoplastic findings, suggesting that in a FIT-positive population their presence may reflect other conditions causing intestinal bleeding rather than underlying neoplasia. Microbial profiles were predominantly associated with distal rather than proximal lesions. Together, our findings highlight the potential for microbial markers to improve FIT-based CRC screening, especially by differentiating those with premalignant lesions from those who test FIT-positive for other reasons.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
Female
Feces/microbiology
Male
*Gastrointestinal Microbiome/genetics
Middle Aged
*Early Detection of Cancer/methods
Aged
Occult Blood
Bacteria/genetics/classification/isolation & purification
Norway
Metagenome
Precancerous Conditions/diagnosis/microbiology
Mass Screening/methods

@article {pmid42642400,
year = {2026},
author = {Liao, H and Ai, C and Liu, C and Zhang, H and Zhang, D and Li, P and Tang, X and Liang, X and Friman, VP and Delgado-Baquerizo, M and Zhou, S},
title = {Carbohydrate-active enzymes of soil prophages enhance global carbon cycling potential.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42642400},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Prophages/enzymology/genetics ; *Carbon Cycle ; Lignin/metabolism ; Metagenome ; Soil/chemistry ; Carbon/metabolism ; Bacteria/genetics/virology/metabolism ; *Viral Proteins/metabolism/genetics ; Mixed Function Oxygenases/metabolism/genetics ; Genome, Bacterial ; },
abstract = {Recent work suggests that soil-borne viruses play an important role in controlling carbon (C) cycling and stocks. However, the contribution of individual prophage (i.e., temperate phages residing within bacterial hosts during lysogenic cycle) to C degradation remains largely undocumented at global scale. Here, we generated a global gene catalog of prophage-encoded carbohydrate-active enzyme (pCAZymes), including 20,131 soil bacterial genomes, 3548 metagenomes, and 951 metatranscriptomes derived from pre-existing databases. The catalog includes 4708 pCAZymes associated with the degradation of lignocellulose, lignin, and pectin, with 21 lytic polysaccharide monooxygenase genes newly identified in phages. Our findings reveal that prophages have potential to accelerate labile soil C degradation by encoding pCAZymes that cooperate with their bacterial hosts. Using machine learning models, we predict a 13 ± 0.7% increase in the C metabolic potential driven by soil prophages by 2100 under a high-emission scenario (SSP585). In vitro experiments demonstrated that the transcriptional activity of pCAZyme genes is regulated by environmental temperature. Soil microcosm experiments further confirmed that pCAZymes can enhance host-mediated organic C mineralization by increasing degradative enzyme activity. This study reveals previously overlooked ecological functions of prophages in global soil C transformation, with important implications for the global climate and C cycling.},
}

*Soil Microbiology
*Prophages/enzymology/genetics
*Carbon Cycle
Lignin/metabolism
Metagenome
Soil/chemistry
Carbon/metabolism
Bacteria/genetics/virology/metabolism
*Viral Proteins/metabolism/genetics
Mixed Function Oxygenases/metabolism/genetics
Genome, Bacterial

@article {pmid42642466,
year = {2026},
author = {Johnstone, N and Cohen Kadosh, K},
title = {Empirical evidence for gut microbial influence on human brain neurochemistry via the gut-brain axis.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42642466},
issn = {1476-5578},
abstract = {The gut microbiome produces metabolites with potential neuroactive properties, many of which act locally within the gut. While preclinical studies suggest these microbial pathways can influence cognitive and emotional processes, human evidence remains limited. This study investigates associations between gut microbiome-derived neuroactive functional potential and in vivo brain neurotransmitter concentrations in healthy young females. Using proton magnetic resonance spectroscopy ([1]H-MRS), we quantified GABA and glutamate levels in the dorsolateral prefrontal cortex (dlPFC), anterior cingulate cortex (ACC), and inferior occipital gyrus (IOG). Parallel metagenomic profiling characterised microbial functional potential for pathways related to the synthesis and degradation of GABA, glutamate, short-chain fatty acids (SCFAs), p-cresol, and inositol. Region-specific associations were observed between these microbial pathways and cortical GABA and glutamate levels, including excitatory/inhibitory (E/I) balance, a key marker of neuroplasticity and mental health. Notably, microbial glutamate degradation and inositol synthesis potential were associated with IOG E/I balance, while additional pathways including GABA metabolism, p-cresol production, and SCFA synthesis showed distinct associations across regions. Exploratory analyses also identified links between microbial functional potential and anxiety, depressive symptoms, and sleep quality. Together, these findings provide new human evidence that variation in microbial functional potential corresponds with regional cortical neurochemistry and psychological wellbeing, highlighting the gut-brain axis as a promising avenue for mechanistically informed microbiome-based- interventions.},
}

@article {pmid42642622,
year = {2026},
author = {Bushnell, B and Villada, JC},
title = {Deployable high-fidelity metagenome binning at scale with QuickBin.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42642622},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Algorithms ; *Metagenome ; *Software ; Microbiota/genetics ; },
abstract = {Reconstructing genomes from metagenomic assemblies is foundational to microbiome research, yet binning faces a persistent trade-off between fidelity and throughput. Many high-accuracy methods rely on GPU-intensive workflows, marker-gene postprocessing, or heavy computational resources, limiting reproducible use at scale. Here, we present QuickBin, a CPU-native, marker-free binning algorithm designed to recover near-complete, ultra-low-contamination metagenome-assembled genomes (MAGs) efficiently. QuickBin pairs a GC-coverage spatial index (BinMap) with an early-exit Oracle cascade of similarity tests (scalar composition/coverage filters and SIMD-accelerated k-mer comparisons), reserving a compact neural network exclusively for ambiguous merges. Across synthetic communities, evaluated by marker-based and contig-origin ground truth, QuickBin maximizes high-fidelity sequence recovery. In benchmarking 297 diverse real metagenomes, QuickBin completed all runs, recovering more high-quality MAGs (≥95% completeness, ≤1% contamination) than resource-intensive alternatives that frequently failed. QuickBin provides a practical path to reproducible, genome-resolved metagenomics at scale for downstream comparative analyses. Open-source at: https://github.com/bbushnell/BBTools .},
}

*Metagenomics/methods
*Algorithms
*Metagenome
*Software
Microbiota/genetics

@article {pmid42643400,
year = {2026},
author = {Medaglia-Mata, A and Rojas-Rodríguez, P and Bystrý, V and Guillén-Watson, R and Gómez-Espinoza, O and Núñez-Montero, K},
title = {PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1909327},
pmid = {42643400},
issn = {2673-7647},
abstract = {BACKGROUND: Environmental microbiome research has advanced through three complementary sequencing modalities, targeted 16S rRNA amplicon sequencing, whole-genome shotgun (WGS) metagenomics, and long-read full-length 16S rRNA profiling, each supported by distinct toolsets with heterogeneous outputs, variable configurations, and different levels of reproducibility documentation. Existing pipelines are typically modality-specific, require substantial configuration expertise, or produce outputs that need further custom scripting before standard ecological analyses can begin. This analytical fragmentation introduces avoidable technical variability and complicates cross-study reproducibility and comparability. PUDU addresses this by integrating all three modalities into a single reproducible workflow with simplified configuration, harmonized outputs across classifiers, and direct compatibility with downstream ecological analysis frameworks.

RESULTS: We present PUDU (Pipeline for Universal Diversity Unveiling), a modular Snakemake workflow that supports amplicon (short-read 16S), shotgun metagenomics (WGS), and long-read 16S analyses from raw reads to standardized outputs for downstream microbial ecology. PUDU performs technology-aware preprocessing and centralized quality control, and integrates established taxonomic approaches, including DADA2 for amplicons, Emu for full-length 16S long reads, and Kraken2/Bracken and Centrifuger for WGS. Across methods, PUDU produces harmonized count and relative-abundance tables at user-defined taxonomic ranks, Krona files, and a standardized Phyloseq-compatible R object to streamline diversity analyses and statistical workflows. PUDU also provides an integrated Shiny interface for metadata-aware alpha/beta diversity, ordination, community composition, and shared-taxa exploration with exportable figures and taxa tables. We demonstrate PUDU on two publicly available environmental datasets spanning rhizosphere WGS and long-read marine sediment 16S, yielding broadly consistent community-level patterns across classifiers (Spearman ρ = 0.936 at phylum level; PERMANOVA R[2] = 0.87-0.95) with peak memory below 45 GB on a standard Linux workstation.

CONCLUSION: PUDU is an end-to-end, reproducible, and extensible framework that enables standardized taxonomic profiling and ecology-oriented analysis across sequencing modalities. By combining harmonized outputs, Phyloseq interoperability, and an integrated visualization layer, PUDU facilitates reproducible, standardized, and comparable environmental microbiome analysis from raw reads to interpretable ecological insights.},
}

@article {pmid42643414,
year = {2026},
author = {Kelly, JJ and Gaisser, K and Drummond, JD and Gonçalves, J and Bernal, S and Martí, E},
title = {Wastewater treatment plant effluent alters particle-associated bacterial assemblages in an intermittent stream.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1880555},
pmid = {42643414},
issn = {1664-302X},
abstract = {Wastewater Treatment Plants (WWTPs) can be point-sources of nutrients, organic matter, anthropogenic contaminants, and microbes to lotic environments, and the input of WWTP effluent can alter the activity and composition of stream microbial assemblages in the benthos and water column. Within the stream benthos, fine particulate matter (FPM) supports especially high levels of microbial activity, but the effect of WWTP effluents on the microbial communities specifically associated with benthic FPM in rivers has not been studied. The present work sought to address this knowledge gap by analyzing FPM quantity, nutrient content, microbial activity, and bacterial assemblage composition in FPM samples collected from sites upstream and downstream of a WWTP effluent input into an intermittent Mediterranean stream. Sampling was conducted on two sampling dates (November and July) and the study included both amplicon and metagenomic sequencing in order to assess both the taxonomic and functional gene composition of the particle-associated bacterial assemblages. Effluent input resulted in increased FPM concentration and increased nutrient content of FPM, which were both correlated with an increase in microbial metabolic activity (MMA) immediately downstream of the WWTP. Effluent was a significant source of bacterial taxa to the stream, and there was a significant decrease in the diversity of the bacterial assemblages associated with the fine particles immediately downstream, as well as changes in their taxonomic and functional gene profiles. Taxa associated with wastewater treatment (Rhodocyclaceae and Xanthomonadaceae) and the metabolism of anthropogenic contaminants (Sphingobacteriales), and genes associated with multidrug efflux pumps and denitrification were more abundant immediately downstream. The effect of effluent on the taxonomic composition of the bacterial assemblages was much stronger than the effect on functional gene profiles, highlighting the functional redundancy within these communities. In addition, all the effects of effluent were short-lived and decreased with distance downstream, especially in November when the upstream flow moderated the effects of effluent. This study indicates that WWTP effluent impacts natural microbial communities by altering environmental conditions and sourcing new microbes but also demonstrates the functional redundancy and resilience of these communities.},
}

@article {pmid42643498,
year = {2026},
author = {Osborn, LJ and Akkad, A and Nanda, N},
title = {Cell-free DNA metagenomic next generation sequencing for the diagnosis of infectious diseases: a retrospective assessment of clinical utility in a tertiary and quaternary care facility.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1879762},
pmid = {42643498},
issn = {1664-302X},
abstract = {BACKGROUND: We sought to retrospectively assess the clinical utility of a commercially available plasma cell-free DNA (cfDNA) metagenomic next generation sequencing (mNGS) known as the Karius test (KT), for the diagnosis of infectious diseases, stratified by clinical syndrome.

METHODS: Retrospective chart review and abstraction were performed to assess the clinical impact of KT. Descriptive statistics were used to characterize the results of the KT in conjunction with host parameters.

RESULTS: This study included 120 KT results from 114 patients, collected from September 1, 2021, through August 31[st], 2024, at our academic medical center which includes a 401-bed acute care, academic hospital offering quaternary care, in addition to a 60-bed cancer hospital. The KT demonstrated clinical utility in 28.3% of all 120 cases, with 67.5% yielding no impact, 2.50% negative impact, and 1.67% indeterminate impact, though impact proportions were syndrome dependent. Host immune competency was not a reliable predictor of KT impact, consistent with previous studies. Overall, the KT yielded 100 unique organisms with a 67.5% positivity rate.

CONCLUSION: Taken together, these data suggest that despite the relatively high rate of organism detection by KT, clinical impact is modest. Based on effect size analyses, this study identified several clinical scenarios that warrant larger scale prospective investigation to more completely elucidate high-yield use cases of KT.},
}

@article {pmid42643532,
year = {2026},
author = {Xiao, Q and Chen, J and Xu, Z and Wu, Q and Jiang, H and Zhang, J and Deng, H and Liu, H},
title = {Campylobacter jejuni-Associated Lumbar Vertebral Osteomyelitis with Cauda Equina Syndrome in the Absence of Gastrointes Symptoms: A Rare Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {618362},
pmid = {42643532},
issn = {1178-6973},
abstract = {BACKGROUND: Campylobacter jejuni (C. jejuni) is a common cause of self-limiting gastroenteritis but rarely causes extraintestinal infections. Vertebral osteomyelitis due to this pathogen is exceptionally uncommon, and cases presenting without gastrointestinal symptoms are even rarer. To our knowledge, no previous case has described lumbar osteomyelitis with a spinal extradural abscess leading to cauda equina syndrome in the absence of enteric symptoms. Diagnosing and managing this infection remains clinically challenging.

CASE PRESENTATION: A 65-year-old man presented with a two-month history of intermittent low back pain, bilateral lower limb numbness and pain, urinary frequency, and constipation. He had one episode of fever before admission but no gastrointestinal symptoms. Magnetic resonance imaging (MRI) showed lumbar (L4/5) osteomyelitis with an epidural abscess compressing the cauda equina. The patient underwent L4/5 partial laminectomy and debridement of the spinal canal abscess. Conventional cultures of preoperative blood and intraoperative specimens were negative. Metagenomic next-generation sequencing (mNGS) of both blood and surgical samples identified C. jejuni as the causative pathogen. Antibiotic susceptibility testing was not available. The patient initially received empirical antibiotics but developed recurrent fever. Treatment was switched to intravenous meropenem and levofloxacin, followed by oral levofloxacin for six weeks, completing a nine-week course. At two-year follow-up, MRI confirmed complete resolution of the infection and the patient made a full recovery.

CONCLUSION: C. jejuni should be considered in spinal infections even without gastrointestinal symptoms. mNGS is useful when cultures are negative. For cases failing initial antibiotics, meropenem plus levofloxacin may be an option, though further data are needed.},
}

@article {pmid42643606,
year = {2026},
author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Ravin, NV},
title = {Metagenomic insights into microbial communities of terrestrial mud volcanos: functional diversity of subsurface archaea and bacteria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1892847},
pmid = {42643606},
issn = {1664-302X},
abstract = {Terrestrial mud volcanoes are surface geological features where fluidized sediments and gasses from the subsurface are discharged along a fracture network providing a window into the deep biosphere. Although mud volcanoes constitute an important source of methane emission from natural environments, their microbial communities responsible for methane cycling remain poorly characterized. Using a metagenomics approach, we investigated the taxonomic composition and metabolic potential of microbial communities in three active mud volcanoes in the Kerch-Taman mud volcanic province. Despite the volcanoes' close proximity their microbial communities strongly differ. In the Kmv1 and Kmv2 volcanoes surface horizons mostly harbored organotrophic microbial communities, while the relative abundance of anaerobic methanotrophic archaea (ANME) increased with depth. The deep horizons (1.5 m) of Kmv1 were dominated by Ca. Methanoperedenaceae that lacked nitrate reductase and could couple methane oxidation to the reduction of metal oxides, while the abundance of sulfate-reducing bacteria was low. Consistently, with higher sulfate content, the deep horizon in Kmv2 was dominated by Ca. Methanoperedenaceae, ANME-2a/2b clade, sulfate-reducing Desulfobacterota and sulfur-oxidizing Gammaproteobacteria. No clear depth distribution of taxa was observed in the Kmv3 volcano where microorganisms of the methane and sulfur cycles, namely, methanogens, ANME-3 clade, methanotrophic bacteria, and sulfate reducers were simultaneously detected. A high-quality genome of a member of the archaeal candidate phylum EX4484-52 within the DPANN lineage was assembled from metagenomes. This archaeon, named Candidatus Lutivulcanarchaeum fermentans, has complete glycolytic pathway and ATP generation mechanisms, but lacked the biosynthetic pathways for many key cellular compounds, indicating a parasitic or symbiotic lifestyle.},
}

@article {pmid42643608,
year = {2026},
author = {Tayyaba, S and Amin, A and Zulfiqar, S and Ahmed, I},
title = {Genome-resolved insights into hydrocarbon-transforming and nitrate-reducing microbial communities from deep petroleum reservoir cores of the Nashpa Oil Field, Pakistan.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1899441},
pmid = {42643608},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial communities from deep subsurface petroleum reservoirs are adapted to hydrocarbon-rich, oxygen-limited, and physicochemically extreme environments. However, genome-resolved knowledge of petroleum reservoir microbiomes from Pakistan remains largely unexplored.

METHODS: Shotgun metagenomic sequencing was used to investigate the functional and metabolic potential of microbial communities inhabiting deep subsurface petroleum reservoir cores from the Nashpa Oil Field, Pakistan, at depths of 3,770-4,315 m. Metagenome-assembled genomes (MAGs) were reconstructed and functionally annotated to assess taxonomic composition and predicted metabolic capabilities.

RESULTS: A total of 402 metagenome-assembled genomes (MAGs) were recovered, of which 216 were high-quality MAGs (≥90% completeness and ≤5% contamination). Taxonomic analysis showed dominance of Pseudomonadota and Actinobacteriota,, including genera such as Alcanivorax, Marinobacter, Pseudomonas, Rhodococcus, and Thermohalobaculum. Functional annotation revealed genes involved in hydrocarbon transformation, nitrate-linked respiration, oxygen-limited metabolism, oxidative phosphorylation, aromatic compound degradation, and cellular stress-response systems. However, markers of hydrocarbon degradation were detected only in a small subset of MAGs, suggesting taxon-specific metabolic specialization rather than broad community-wide enrichment. Genes associated with nitrate reduction and microaerophilic or anaerobic respiration suggested metabolic flexibility under the variable oxygen conditions typical of deep petroleum reservoirs. Stress-associated genes, including molecular chaperones and heat-shock proteins, further indicated putative adaptation to reservoir-associated environmental stress, although thermotolerance was not experimentally confirmed.

DISCUSSION: This study provides one of the first genome-resolved insights into deep petroleum reservoir microbiomes from Pakistan and identifies candidate microbial lineages carrying MEOR-relevant genomic traits for future functional validation.},
}

@article {pmid42643757,
year = {2026},
author = {Raphael, D and Parthasarathi, T},
title = {Halophilic plant growth-promoting bacterial consortium reshapes soil microbiota to enhance salinity tolerance, antioxidant defense, and yield in Vigna mungo L.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1878014},
pmid = {42643757},
issn = {1664-302X},
abstract = {Soil salinity is a major abiotic stress that severely restricts crop productivity by disrupting ionic balance, inducing osmotic stress, and promoting oxidative damage. Black gram (Vigna mungo L.), an important pulse crop, is highly sensitive to salinity, resulting in reduced growth, physiological performance, and yield. The present study evaluated the efficacy of a compatible multi-strain HPGPB consortium comprising MKM3 (Halobacillus marinus), MKM4 (Halobacillus halophilus), and MKM11 (Halobacillus halophilus) in enhancing salinity tolerance in two black gram varieties (VBN8 and VBN11) under greenhouse conditions. Plants were subjected to 50 and 100 mM NaCl stress, with and without consortium inoculation, in a completely randomized design. Salinity stress significantly reduced plant growth, photosynthetic pigments, biomass, nutrient uptake, and grain yield, while increasing Na[+] accumulation, lipid peroxidation, and osmotic stress markers. Consortium inoculation effectively mitigated these adverse effects by improving plant height, root development, biomass, and grain yield by up to 46 and 38%, respectively, under saline conditions. Consortium-inoculated plants exhibited improved photosynthetic performance, enhanced nutrient uptake and ionic balance, reduced Na[+] accumulation and malondialdehyde content, and increased activities of antioxidant enzymes, indicating enhanced salinity tolerance. Among the tested varieties, VBN11 exhibited greater salinity tolerance and a stronger response to consortium inoculation than VBN8. Rhizosphere metagenomic analysis revealed consortium-associated shifts in microbial community structure under saline conditions. Collectively, the results demonstrate that the HPGPB consortium enhances salinity tolerance through coordinated physiological, biochemical, and microbiome-associated mechanisms. These findings highlight the potential of HPGPB consortia as sustainable bioinoculants for improving black gram productivity in salt-affected agroecosystems.},
}

@article {pmid42644084,
year = {2026},
author = {Conselheiro, JA and Moreira, FRR and Barone, GT and Reis-Menezes, AA and da Rosa, AR and de Oliveira, DC and Chaves, BA and de Souza Sampaio, V and Rocha, F and Vigilato, MAN and Stabeli, RG and do Carmo Said, RF and Brandão, PE and Wallau, GL and de Brito, AF},
title = {Viral metagenomics of synanthropic urban bats: A surveillance strategy for uncovering potentially zoonotic viruses.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101549},
pmid = {42644084},
issn = {2352-7714},
abstract = {Bats are natural reservoirs for diverse viruses, including coronaviruses, filoviruses, and paramyxoviruses, several of those known to be involved in zoonotic spillover events and demanding an integrated surveillance. Here, we present a framework that leverages Brazil's rabies passive surveillance programme to detect bat-borne viruses. Using an algorithm to select representative specimens from 2422 bats collected across São Paulo state, we submitted 150 paired lung and intestine samples to nanopore metagenomic sequencing. We detected 98 viral contigs from 12 families of public health relevance, including Arenaviridae, Coronaviridae, and Paramyxoviridae. Notably, the approach identified a previously unknown filovirus in bats in the Americas, validating the framework's capacity for epidemic preparedness. These findings reveal an undetected viral diversity and demonstrate how existing animal surveillance can monitor pathogen threats. Crucially, in a workshop involving multisectoral One Health experts in Brazil, this framework was validated as a scalable model for national expansion, adapted for low- and middle-income countries (LMICs).},
}

@article {pmid42644416,
year = {2026},
author = {Cavani, E and Edbom Devall, A and Chen, Y and Grompone, G and Brusselaers, N and Vlajic, M and de Vos, WM},
title = {Nationwide cohort study reveals low bifidobacteria and distinct microbiota composition and function in Swedish newborns.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2719244},
doi = {10.1080/19490976.2026.2719244},
pmid = {42644416},
issn = {1949-0984},
mesh = {Humans ; *Bifidobacterium/isolation & purification/classification/genetics/physiology ; Infant, Newborn ; Sweden ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Female ; },
abstract = {NCT06285630.},
}

Humans
*Bifidobacterium/isolation & purification/classification/genetics/physiology
Infant, Newborn
Sweden
*Gastrointestinal Microbiome
Feces/microbiology
Cohort Studies
Female

@article {pmid42644746,
year = {2026},
author = {Zhang, E and Li, S and Tan, E and Jiang, Q and Li, Y and Wu, Z and Chen, J and Wan, X and Lin, X and Chen, N and Cong, Y and Jiao, N and Dong, X and Zheng, Q},
title = {Metabolic division of labour drives estuarine-coastal N2O emissions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag216},
pmid = {42644746},
issn = {1751-7370},
abstract = {Estuarine and coastal systems are global hotspots of marine nitrous oxide (N2O) emissions, where microbial nitrification and denitrification are the primary processes regulating N2O dynamics. However, how interactions among different N2O-associated microorganisms influence ecosystem-scale N2O emissions remains poorly understood. This study combined in situ N2O concentrations, 15N-based potential rates, metagenomics, metatranscriptomics, and genome-scale metabolic model analysis to explore N2O production and reduction processes in estuarine and coastal systems. Potential N2O production and reduction rates, together with in situ concentrations, the relative abundance, and the transcriptional activity of associated genes, were significantly higher at low salinity and declined toward coastal regions. Based on the gene content of 974 recovered N2O-associated genomes, microorganisms were classified into three functional groups: net N2O producers, net N2O consumers, and self-sustaining N2O players. The abundance, composition, and activity of these functional groups shifted along estuarine-coastal gradients. A larger NO/N2O exchange gap, reflecting the imbalance between model-inferred NO and N2O handoff potentials, was found at low salinity and was associated with elevated bottom-water N2O concentrations. Together, community-level division of labour and the associated exchange gap provide a conceptual framework for linking N2O-related functional groups to N2O accumulation in estuarine-coastal ecosystems.},
}

@article {pmid42644751,
year = {2026},
author = {Liu, J and Zhou, G and Chen, L and Xiao, Y and Kuzyakov, Y and Zhang, C and Huang, P and Ma, D and Zhang, J},
title = {Soil amelioration impacts viral ecology in saline-alkali lands.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag217},
pmid = {42644751},
issn = {1751-7370},
abstract = {The continuous expansion of saline-alkali lands under climate change threatens food security and reduces soil carbon stocks. A common mitigation strategy is soil amelioration, which converts degraded soils back into an arable state. Microbes play critical roles in soil health and recovery. However, the viruses that infect these microbial communities, and their potential impacts during saline-alkali soil restoration, remain largely unknown. Here, we combined total soil metagenomics and viromics to investigate host-linked viral ecology across four major saline-alkali regions in China, each encompassing two soil amelioration statuses: saline-alkali and reclaimed. We found that viral community structure was shaped by both geography and soil amelioration status, with salinity and alkalinity emerging as key environmental factors. Viral populations were sensitive to soil restoration, showing strong amelioration-status endemism with functional adaptations. Virus-host dynamics ranged from reduced temperate viruses to abundance mismatches in those infecting key carbon-cycling microorganisms, including carbohydrate degraders. 13C-cellulose DNA-SIP experiments provided further support for this mismatch by tracing assimilated carbon transfer between active host and virus populations. Compared with saline-alkali soils, the relative abundance of hosts in restored soils increased from 39.0% to 61.0%, whereas the linked viruses decreased from 60.6% to 39.4%. Together, these findings reveal an underappreciated role of viruses in shaping saline-alkali soil amelioration trajectories, and could improve management strategies for degraded land recovery and carbon storage.},
}

@article {pmid42644888,
year = {2026},
author = {Dalibayeva, G and Goremykina, M and Kozhakhmetov, S and Kushugulova, A and Kossumov, A and Kalmakhanov, S and Doszhan, A},
title = {Reproducible Gut Microbiome Alterations in Major Depressive Disorder: A Systematic Review of Taxonomic and Functional Findings.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {7},
number = {4},
pages = {},
doi = {10.3390/epidemiologia7040104},
pmid = {42644888},
issn = {2673-3986},
abstract = {BACKGROUND/OBJECTIVES: Major depressive disorder (MDD) has been increasingly associated with alterations of the gut microbiome through the microbiota-gut-brain axis. However, published findings remain highly heterogeneous, limiting identification of reproducible microbial signatures associated with depression. This systematic review aimed to evaluate reproducible taxonomic and functional gut microbiome alterations in patients with MDD compared with healthy controls.

METHODS: A systematic literature search was conducted in PubMed/MEDLINE, Scopus, Web of Science Core Collection, and the Cochrane Library for studies published between January 2016 and December 2025. Observational human studies evaluating gut microbiome composition in adults with clinically diagnosed MDD and healthy control groups were included. Methodological quality was assessed using the Newcastle-Ottawa Scale. Due to substantial methodological heterogeneity, findings were synthesized using structured qualitative narrative analysis.

RESULTS: Sixteen observational studies were included in the qualitative synthesis. Findings related to alpha diversity were inconsistent across studies, whereas beta diversity alterations demonstrated greater reproducibility across independent cohorts. The most recurrent microbiome pattern involved depletion of short-chain fatty acid (SCFA)-producing bacteria, particularly Faecalibacterium and Roseburia, together with recurrent alterations affecting members of the Ruminococcaceae, Lachnospiraceae, and Clostridia groups. Functional microbiome alterations demonstrated greater consistency than higher-level taxonomic findings and included reduced butyrate synthesis pathways, dysregulated amino acid and tryptophan metabolism, increased lipopolysaccharide biosynthesis, and enrichment of pro-inflammatory microbial signatures. Antidepressant-naïve cohorts generally demonstrated more homogeneous dysbiosis patterns than mixed-treated populations.

CONCLUSIONS: Current evidence suggests that functional gut microbiome dysregulation may represent a more reproducible biological feature of MDD than isolated taxonomic alterations alone. However, substantial heterogeneity in study design, participant characteristics, sequencing methodologies, and analytical approaches continues to limit clinical translation. Large-scale longitudinal multi-omics studies using standardized methodologies are required to clarify the role of the gut microbiome in depressive disorders and to evaluate the potential utility of microbiome-based biomarkers and interventions in mental health and public health practice.},
}

@article {pmid42646092,
year = {2026},
author = {Yin, Y and Zhao, Y and Zhao, M and Zhang, L and Li, R and Liu, L},
title = {Molecular Mechanisms, Diagnosis, and Therapeutic Strategies of Antifungal Resistance in Filamentous Fungi.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/jof12080565},
pmid = {42646092},
issn = {2309-608X},
support = {25ZXZSSS00350//National Key Laboratory Major Special Project/ ; },
abstract = {Antifungal resistance in filamentous fungi has emerged as a major threat to global public health, posing a serious challenge particularly to immunocompromised populations. This review provides a systematic overview of the molecular mechanisms, diagnostic approaches, and clinical therapeutic strategies for antifungal resistance in filamentous fungi, with a focus on Aspergillus fumigatus, Fusarium spp., Mucorales, and Scedosporium spp./Lomentospora prolificans. Resistance mechanisms can be broadly categorized as intrinsic resistance and acquired resistance. Intrinsic resistance arises from species-specific genetic traits, such as structural differences in target sites, constitutive overexpression of efflux pumps, and metabolic pathway redundancy. Acquired resistance develops under drug pressure through target gene mutations (e.g., hotspot mutations and promoter tandem repeats in CYP51A), efflux pump overexpression, biofilm formation, and epigenetic regulation. For diagnosis, conventional culture and antifungal susceptibility testing remain the gold standard; however, molecular techniques-including MALDI-TOF MS, targeted resistance gene PCR, and metagenomics-are substantially improving detection efficiency. Therapeutic strategies should be stratified based on antifungal susceptibility testing results and species identification. Precision dosing guided by therapeutic drug monitoring, combination therapy, and the introduction of novel agents (including isavuconazole, rezafungin, fosmanogepix, and olorofim) are progressively improving clinical outcomes. Looking ahead, global surveillance and multisectoral collaboration are essential to deepen our understanding of resistance evolution, accelerate the clinical translation of novel diagnostic and therapeutic tools, and curb the global spread of resistance.},
}

@article {pmid42646328,
year = {2026},
author = {Jia, Y and Gao, B and Wu, K and Gao, M and Lin, Q and Qian, T and Ma, J and Zhang, H and Zhu, P and Chen, Z and Zhai, Y},
title = {Cold-Induced Elevation of 3-Hydroxypropionate Exacerbates Colitis by Remodeling Gut Microbiota and Impairing Mitochondrial Respiration in Intestinal Epithelial Cells.},
journal = {Metabolites},
volume = {16},
number = {8},
pages = {},
pmid = {42646328},
issn = {2218-1989},
support = {82322029//National Natural Science Foundation of China/ ; 32541024//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder influenced by environmental factors including cold stress. While cold exposure exacerbates intestinal inflammation, the specific microbial metabolites linking environmental stress to colitis remain unclear. 3-Hydroxypropionate (3-HPA) is a gut microbial metabolite elevated following cold exposure, but its pathogenic role in intestinal inflammation has not been investigated. This study aimed to determine whether 3-HPA contributes to colitis progression and to characterize its effects on gut microbiota and intestinal epithelial function.

METHODS: We employed a dextran sulfate sodium (DSS)-induced colitis mouse model to assess the impact of cold exposure and exogenous 3-HPA administration. Paired shotgun metagenomic and metabolomic analyses were performed to evaluate gut microbial composition and metabolic outputs. Mechanistic studies using NCM460 intestinal epithelial cells were conducted to examine mitochondrial respiration and tight junction integrity under nutrient-limited conditions.

RESULTS: Cold exposure increased fecal 3-HPA levels and aggravated DSS-induced colitis, characterized by enhanced weight loss, histological damage, and immune cell infiltration. Direct 3-HPA supplementation alone was sufficient to worsen colitis severity. Multi-omics profiling revealed that 3-HPA reshaped gut microbiota composition, depleted short-chain fatty acids (SCFAs), and disrupted microbial tryptophan and bile acid metabolism. In vitro, 3-HPA impaired mitochondrial oxidative phosphorylation, reduced ATP production, and compromised tight junction organization in intestinal epithelial cells.

CONCLUSIONS: These findings identify 3-HPA as a gut microbial metabolite elevated by cold exposure that contributes to colitis progression by disrupting beneficial microbial metabolism while also impairing epithelial mitochondrial function and barrier integrity. Modulating 3-HPA production or its downstream epithelial effects may represent a potential therapeutic approach for IBD exacerbated by environmental stress.},
}

@article {pmid42647084,
year = {2026},
author = {Díaz-Díaz, LM and Estremera-Rodriguez, L and Rojas-Correa, M and Quintana, MDC and Madziar, C and Hickey, DC and Vargas Robles, D and Méndez, Y and Santiago, A and Bermudez, D and Olendzki, B and Torres, EA and Maldonado-Contreras, A},
title = {Diet quality, gut microbiome, and inflammatory signatures in Puerto Rican adults with Crohn disease: a multidimensional analysis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag161},
pmid = {42647084},
issn = {1536-4844},
support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
abstract = {BACKGROUND AND AIMS: Diet is increasingly recognized as a modifiable factor influencing gut microbiome and outcomes in Crohn disease (CD), yet data in underrepresented populations remain limited. We evaluated diet quality, dietary patterns, gut microbiome composition, inflammatory markers, and patient-reported outcomes in adults with CD from Puerto Rico.

METHODS: We conducted a cross-sectional analysis of 60 adults with CD enrolled prior to dietary intervention in a parent study. Dietary intake was assessed using 24-hour recalls and evaluated using the Healthy Eating Index-2015 (HEI-2015), Alternative Healthy Eating Index-2010 (AHEI-2010), and exploratory dietary pattern analysis. The gut microbiome was assessed by shotgun metagenomic sequencing. Clinical outcomes included fecal calprotectin, C-reactive protein (CRP), a 96-cytokine panel, short Crohn Disease Activity Index (sCDAI), and short Inflammatory Bowel Disease Questionnaire (sIBDQ). Associations were evaluated using unadjusted and adjusted models with false discovery rate (FDR) correction.

RESULTS: Overall diet quality was poor and characterized by low intake of fruits, vegetables, whole grains, and fiber, alongside high intake of saturated fat, added sugars, and animal-derived protein. Four dietary patterns were identified: vegetable-rich, dairy-rich, fruit-rich, and coffee/sweetener-rich. Participants adhering to the fruit-rich pattern exhibited the highest diet quality scores. Higher HEI-2015 scores were associated with greater gut microbial diversity and differences in overall microbiome composition. Participants with greater adherence to the vegetable-rich pattern showed modest increases in microbial diversity. Exploratory analyses suggested that higher fruit intake and adherence to a fruit-rich dietary pattern were associated with lower fecal calprotectin and CRP levels, whereas adherence to a vegetable-rich pattern was associated with better health-related quality of life (HRQoL) and adherence to a coffee/sweetener-rich pattern was associated with a worse symptom burden. However, no associations between dietary metrics and inflammatory markers, cytokines, or clinical outcomes remained significant after FDR correction. Most participants were in clinical remission despite substantial impairment in HRQoL.

CONCLUSIONS: Adults with CD in Puerto Rico exhibited poor diet quality that was associated with gut microbial diversity and exploratory differences in clinical outcomes. While these findings support the influence of diet on the microbiome and clinical outcomes, larger longitudinal studies are needed to determine whether dietary improvements can influence disease outcomes this underrepresented population.},
}

@article {pmid42637196,
year = {2026},
author = {Zhao, L and Wei, S and Zhang, Y and Tao, L and Xu, Y and Wang, Y and Hu, Z and Tang, J and Wang, S},
title = {Engineering Chlorella-based consortia for sustainable food wastewater treatment: nutrient recovery, pollutant degradation and advanced harvesting.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125549},
doi = {10.1016/j.envres.2026.125549},
pmid = {42637196},
issn = {1096-0953},
abstract = {Microalgae-based bioremediation of wastewater enables simultaneous nutrient removal and production of value-added biomass. This study systematically evaluated three geographically distinct Chlorella sp. strains for semi-continuous treatment of food wastewater, addressing critical challenges that hinder practical application. All strains demonstrated substantial nutrient removal (NO3[-]-N > 73%, TP > 78%), with film-forming Chlorella sp. CQ uniquely sustaining complete nitrate elimination. This strain simultaneously produced biomass in which essential amino acids accounted for 40% of total amino acids, showing both operational stability and nutraceutical potential. Metagenomic profiling of the associated bacterial community in Chlorella sp. CQ culture revealed complementary contributions to nutrient removal, involving cyanobacterial photosynthetic carbon fixation, nitrogen assimilation and denitrification. To address harvesting challenges, biofilm formation on carriers and hydrogel immobilization strategies were implemented. The Chlorella sp. CQ culture with biofilm carriers achieved near-complete biomass sedimentation within 10 hours through induced flocculation, and 1.48-fold increase in maximum biomass accumulation. Notably, both carrier-assisted and hydrogel-based immobilization systems achieved complete degradation of organic pollutants (sodium dodecyl sulfate and organic acids). Transcriptomic analysis of Chlorella sp. CQ under pollutant stress identified upregulation of oxidation-reduction processes, proteasome complex and actin binding as key adaptive responses. This system establishes an integrated approach for sustainable wastewater treatment and resource recovery through microbial consortium selection and advanced harvesting techniques.},
}

@article {pmid42637340,
year = {2026},
author = {Li, Q and Feng, H and Wang, J and Han, L and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Microbial community succession, functional dynamics, and fermentative characteristic of yeasts in the fermented grains of strong-flavor Baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 5},
pages = {120183},
doi = {10.1016/j.foodres.2026.120183},
pmid = {42637340},
issn = {1873-7145},
mesh = {*Fermentation ; *Yeasts/metabolism/classification/genetics ; *Wine/microbiology ; *Food Microbiology ; Taste ; *Microbiota ; *Edible Grain/microbiology ; *Alcoholic Beverages/microbiology ; Ethanol/metabolism ; },
abstract = {To elucidate the succession patterns and functional characteristics of microbial community during the fermentation of Strong-flavor Baijiu, this study integrated metagenomics, flavor analysis, and pure culture approaches to systematically investigate the dynamic changes in the microecosystem of fermented grains over 0-60 days of fermentation. In addition, the fermentative performance and environmental adaptability of the core yeast strains were evaluated. The results showed that Daqu-derived microorganisms (e.g., Kroppenstedtia and Rhizopus) dominated the early fermentation stage, whereas lactic acid bacteria (e.g., Lactobacillus and Acetilactobacillus) and yeasts (e.g., Pichia) became predominant in the late stage. Fungal community succession occurred earlier than that of bacteria. Functional annotation revealed that metabolic pathways related to carbohydrate metabolism and pyrimidine biosynthesis continuously increased throughout fermentation, with Firmicutes being the primary contributors. In the middle and late fermentation stages, the abundance of alcohol dehydrogenase (ADH) genes increased significantly, with Saccharomyces and the non-Saccharomyces yeast Pichia being the main contributors. Acidity and ethanol were identified as key drivers shaping microbial community succession, and most flavor compounds, such as ethyl acetate, predominantly accumulated during the middle-to-late fermentation stages. The two non-Saccharomyces yeasts, Pichia kudriavzevii Pk1 and Wickerhamomyces anomalus Wa9, exhibited both robust ethanol fermentation capacity and a desirable metabolic profile characterized by "high ester production with low 3-methyl-1-butanol formation." This study systematically reveals the temporal succession and functional dynamics of the microbial community during strong-flavor Baijiu fermentation and provides valuable microbial resources for targeted fermentation enhancement and the development of functional starter cultures.},
}

*Fermentation
*Yeasts/metabolism/classification/genetics
*Wine/microbiology
*Food Microbiology
Taste
*Microbiota
*Edible Grain/microbiology
*Alcoholic Beverages/microbiology
Ethanol/metabolism

@article {pmid42637407,
year = {2026},
author = {Wang, Q and Zhang, J and Li, J and Borjihan, Q and Wusigale, and Dorjgotov, D and Jambal, T and Tseveen, S and Xia, Y and Chen, Y},
title = {Integrated metagenomics and metabolomics reveal geographical signatures in the microbiome and metabolome of Jiaoke from Inner Mongolia, China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 4},
pages = {120052},
doi = {10.1016/j.foodres.2026.120052},
pmid = {42637407},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; China ; *Metabolomics/methods ; *Microbiota/genetics ; *Metabolome ; *Cultured Milk Products/microbiology/analysis ; Fermentation ; Food Microbiology ; Animals ; Bacteria/classification/genetics/metabolism ; Multiomics ; },
abstract = {Jiaoke is a traditional fermented dairy product from Inner Mongolia, China, and its characteristic flavor and quality attributes are shaped by region-specific microbial communities. In this study, shotgun metagenomic sequencing combined with untargeted metabolomics was used to systematically characterize Jiaoke samples collected from three distinct ecological production regions: Hulun Buir (HLB), Xilingol (XLG), and Bayan Nur (BYN). The results demonstrated pronounced regional specificity in both microbial composition and metabolite profiles across the three regions. BYN samples were dominated by Lactococcus lactis and Bifidobacterium spp. with enrichment of lipid-derived metabolites. HLB samples were characterized by Lactococcus raffinolactis and psychrotolerant bacteria, together with elevated levels of sphingolipids. In contrast, XLG samples were dominated by Streptococcus macedonicus and exhibited high abundances of amino acids and dipeptides. Correlation analysis indicated that Lactococcus raffinolactis and Streptococcus macedonicus may contribute to Jiaoke flavor formation by promoting milk protein hydrolysis and dipeptide accumulation. These findings provide a basis for understanding regional flavor formation, developing tailored starter cultures, and establishing geographically indicated products in the future.},
}

*Metagenomics/methods
China
*Metabolomics/methods
*Microbiota/genetics
*Metabolome
*Cultured Milk Products/microbiology/analysis
Fermentation
Food Microbiology
Animals
Bacteria/classification/genetics/metabolism
Multiomics

@article {pmid42637484,
year = {2026},
author = {Zhou, H and Yan, L and Zhang, L and Wang, R and Xu, S and Xu, B and Wu, X and Li, X},
title = {Insights into the analysis of microbial communities in fermented foods from the perspective of DNA-based techniques.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 4},
pages = {120175},
doi = {10.1016/j.foodres.2026.120175},
pmid = {42637484},
issn = {1873-7145},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology/methods ; Fermentation ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; },
abstract = {The quality, flavor, and stability of fermented foods depend on the microbial community. However, microbial dynamics are difficult to observe directly, leading to limited control over fermentation. High-throughput sequencing is a revolutionary tool for microbial characterization, among which DNA-based amplicon and metagenomic sequencing are core techniques. Nevertheless, the related data processing workflows in the context of fermented foods have not yet been systematically summarized, hindering the translation of research findings into fermentation practices. This review clarifies the applications of amplicon and metagenomic sequencing in fermented foods. For amplicon sequencing, the impacts of target regions, data preprocessing, and reference databases are addressed. For metagenomic sequencing, sequencing strategies, read-based and binning-based analytical methods, functional annotation, and species-specific databases are discussed. In addition, major strategies for downstream analysis of community data are summarized, including microbial diversity, co-occurrence networks, niche and community assembly, key environmental drivers, and machine learning-based prediction. Amplicon sequencing efficiently reveals microbial succession during fermentation but has limitations in functional annotation. Metagenomic sequencing is notable for functional annotation, enabling the linkage between microbial communities and metabolic potential alongside community characterization. Standardized data preprocessing and specific databases are critical for improving characterization. For community data, integrated analysis allows uncovering the driving factors of microbial succession, thereby helping to regulate fermentation. Notably, the compositional nature of the data must be considered and validated to avoid spurious associations. In summary, the exponential growth of sequencing data will propel the era of precision fermentation.},
}

*Fermented Foods/microbiology
*Food Microbiology/methods
Fermentation
High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Microbiota/genetics

@article {pmid42637687,
year = {2026},
author = {Zhang, YY and Ding, XY and Lu, MP and Chen, YB and Yuan, Y and Jiang, L and Zhang, M and Cheng, L},
title = {Microbial-Metabolite Signatures Are Associated With Glucocorticoid Responsiveness in Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70246},
pmid = {42637687},
issn = {2042-6984},
support = {82501376//National Natural Science Foundation of China/ ; BK20241137//Basic Research Program of Jiangsu/ ; 2023GY016//Center for Scientific Research and Development in Higher Education Institutes, Ministry of Education/ ; JSDW202203//Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; YXL-2021-0387-0752//Beijing Medical Award Foundation/ ; },
abstract = {BACKGROUND: Patients with chronic rhinosinusitis with nasal polyps (CRSwNP) exhibit heterogeneous responses to oral glucocorticoids (GCs), but the biological basis of this variability remains unclear.

OBJECTIVE: To identify gut microbiome‒plasma metabolomic signatures associated with GC responsiveness in CRSwNP patients and to compare their predictive value with that of conventional clinical indicators.

METHODS: Patients with CRSwNP aged 18-65 years with bilateral nasal polyps and a nasal polyp score (NPS) ≥ 2 on at least one side were enrolled, together with septoplasty controls without sinonasal disease. GC responsiveness was defined as the change in endoscopic NPS after 2 weeks of oral methylprednisolone. Fecal shotgun metagenomic and untargeted plasma metabolomics were performed.

RESULTS: Twenty-six CRSwNP patients and 30 controls were included. At baseline, GC responders had significantly greater tissue eosinophilic inflammation, whereas GC non-responders had higher NPS. Responders exhibited distinct baseline gut microbial and plasma metabolic profiles, characterized by the enrichment of Bacteroides caccae, Microbacterium flavum, and Mucilaginibacter rigui, and markedly elevated levels of lupinisoflavone N, CAY10622, kanzonol V, and D-sorbitol. These baseline features were positively correlated with tissue eosinophilic inflammation. After treatment, reductions in Lund-Mackay CT total score, ethmoid/maxillary sinus CT score ratio, NPS, tissue eosinophilic inflammation, and tissue IL-6 mRNA levels were significantly greater in GC responders. Tissue eosinophil count was the strongest conventional predictor (AUC = 0.885), while the integrated multiomics model achieved an AUC of 0.899, showing only marginal improvement.

CONCLUSION: Gut microbiome-plasma metabolomic signatures capture the systemic immunometabolic context of GC therapy and are linked to GC responsiveness in CRSwNP, explaining interindividual treatment efficacy differences.},
}

@article {pmid42638134,
year = {2026},
author = {Chen, Y and Wang, H},
title = {Delayed diagnosis of spinal tuberculosis mimicking spondyloarthritis: a case report.},
journal = {Journal of medical case reports},
volume = {20},
number = {1},
pages = {},
pmid = {42638134},
issn = {1752-1947},
support = {2020Y2014//Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma/ ; },
mesh = {Humans ; Female ; *Tuberculosis, Spinal/diagnosis/therapy/diagnostic imaging ; *Delayed Diagnosis ; Diagnosis, Differential ; Aged ; Magnetic Resonance Imaging ; Antitubercular Agents/therapeutic use ; Tomography, X-Ray Computed ; *Spondylarthritis/diagnosis ; Low Back Pain/etiology ; Debridement ; Spinal Fusion ; Treatment Outcome ; Decompression, Surgical ; Lumbar Vertebrae/diagnostic imaging ; },
abstract = {BACKGROUND: Spinal tuberculosis (TB) remains a significant health burden in endemic regions. Its diagnosis is frequently delayed due to non-specific early symptoms and radiological findings that can mimic other inflammatory spinal pathologies, leading to severe complications such as kyphosis and neurological deficit.

CASE PRESENTATION: A 71-year-old woman from Southeast China presented with a 1-year history of progressive low back pain, initially misdiagnosed as axial spondyloarthritis. She experienced temporary relief with symptomatic treatment, including secukinumab. One year later, her symptoms recurred severely. Advanced imaging (computed tomography/magnetic resonance images) revealed destruction of the L1 and L2 vertebral bodies with a paravertebral abscess. Microbiological confirmation was obtained via a positive T-SPOT.TB test and metagenomic next-generation sequencing detecting Mycobacterium tuberculosis complex. The patient successfully underwent posterior debridement, spinal canal decompression, fusion, and instrumentation, followed by a standard anti-tuberculosis regimen. Her symptoms significantly improved, and she resumed return to work within 2 months.

CONCLUSION: This case highlights the potential for spinal TB to masquerade as seronegative spondyloarthritis, leading to dangerous diagnostic delays. Clinicians should maintain a high suspicion for TB in endemic areas and employ specific diagnostic tests early. Timely surgical intervention for instability or neurological compromise, combined with appropriate chemotherapy, is crucial for optimal outcomes.},
}

Humans
Female
*Tuberculosis, Spinal/diagnosis/therapy/diagnostic imaging
*Delayed Diagnosis
Diagnosis, Differential
Aged
Magnetic Resonance Imaging
Antitubercular Agents/therapeutic use
Tomography, X-Ray Computed
*Spondylarthritis/diagnosis
Low Back Pain/etiology
Debridement
Spinal Fusion
Treatment Outcome
Decompression, Surgical
Lumbar Vertebrae/diagnostic imaging

@article {pmid42638477,
year = {2026},
author = {Schlesinger, MS and Dadhania, DM and Lee, JR and De Vlaminck, I},
title = {Precision monitoring of kidney transplant health via cell-free DNA and RNA.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001309},
pmid = {42638477},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: Cell-free nucleic acids (cfNAs) in plasma and urine have emerged as noninvasive biomarkers for monitoring kidney transplant health. This review summarizes recent advances in the development of cell-free DNA (cfDNA) and cell-free RNA (cfRNA) assays for immune and infection-related complications, and discusses their potential to enable precision monitoring of allograft health.

RECENT FINDINGS: Large prospective multicenter studies have established donor-derived cfDNA as a robust biomarker of acute allograft rejection, with increasing evidence supporting the use of cfDNA for surveillance, prognostication, and integration with complementary molecular and clinical biomarkers. Metagenomic cfDNA assays enable broad detection of bacterial, viral, and fungal pathogens. More recently, cfRNA profiling has emerged as a complementary approach that captures tissue-type and cell-type-specific transcriptional activity, providing molecular insight into immune activation, tissue injury, and disease mechanisms. Urine cfRNA is particularly promising because of its enriched representation of kidney-derived transcripts.

SUMMARY: Cell-free nucleic acid assays are reshaping the management of kidney transplant recipients by enabling noninvasive assessment of rejection, infection, and allograft injury. Continued advances in sequencing technologies, computational methods, and multimodal biomarker integration are expected to accelerate their clinical adoption and improve precision care for transplant recipients.},
}

@article {pmid42638640,
year = {2026},
author = {Singh, S and Singh, AK and Kumar, S and Singh, N and Mishra, AK and Mohanty, A},
title = {Advanced diagnostic methods for nontuberculous mycobacterial infections.},
journal = {Frontiers in tuberculosis},
volume = {4},
number = {},
pages = {1760581},
pmid = {42638640},
issn = {2813-7868},
abstract = {Nontuberculous mycobacteria (NTM) represent an increasingly significant cause of pulmonary and extrapulmonary infections, but are sometimes misinterpreted as tuberculosis (TB) owing to overlapping clinical and microbiological characteristics. Conventional diagnostic approaches, such as Ziehl-Neelsen staining and culture in a Mycobacterial Growth Indicator Tube (MGIT) system, are constrained by extended incubation times, are insufficient for accurate species differentiation, and are limited by prolonged incubation periods. Recent molecular and genomic advances have transformed NTM diagnostics by enabling rapid, specific, and high-resolution identification. Line probe assays (e.g., GenoType Mycobacterium CM/AS assay) and multiplex PCR have enhanced the ability to distinguish between NTM species such as Mycobacterium absessus, M. fortuitum, and M. avium complex and M. tuberculosis complex, which is essential for proper treatment and epidemiological mapping. Among newer proteomic platforms, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry has emerged as a transformative, cost-effective technology capable of identifying Mycobacterium species directly from culture isolates through protein fingerprinting. It provides rapid, reproducible, and highly discriminatory identification between closely related species. Next-generation sequencing (NGS) and whole genome sequencing approaches now offer unprecedented insight into species identification, strain typing, and drug-resistance prediction, complementing traditional culture-based susceptibility testing. Newer techniques such as metagenomics NGS (mNGS), targeted NGS (tNGS) multilocus sequence typing, and mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR) genotyping facilitate subspecies-level resolution and real-time outbreak surveillance. Moreover, molecular beacons, insertion sequence analysis, and repetitive sequence-based polymerase chain reaction (Rep-PCR) enhance detection sensitivity even in paucibacillary samples. The integration of genomic data with automated diagnostic system promises earlier intervention, accurate species delineation, and improved patient outcome.},
}

@article {pmid42638692,
year = {2026},
author = {Fourgeaud, J and Neven, B and Kamar, N and Farhat, I and Manuel, O and Sester, M and Couzi, L and Boutboul, D and Zucman, SC and Lelievre, JD and Le Stang, MB and Le Maréchal, M and François, H and Antoine, D and Zuber, J and Kaminski, H},
title = {"Innovative diagnostics and treatments of infections in transplantation," report from the 2025 spring highlights in transplantation sciences meeting.},
journal = {Transplant international : official journal of the European Society for Organ Transplantation},
volume = {39},
number = {},
pages = {16562},
pmid = {42638692},
issn = {1432-2277},
mesh = {Humans ; *Organ Transplantation/adverse effects ; *Virus Diseases/diagnosis/therapy ; Antiviral Agents/therapeutic use ; },
abstract = {Infectious complications remain a leading cause of morbidity and mortality after solid organ transplantation, driven by profound immunosuppression, emerging pathogens, and increasing antiviral resistance. The 2025 Spring Highlights in Transplantation Sciences (HITS) meeting, held in Paris under the auspices of the Société Francophone de Transplantation and endorsed by the European Society of Organ Transplantation, brought together international experts to discuss recent advances in the diagnosis, pathogenesis, prevention, and treatment of infections in transplant recipients. This report summarizes the key scientific presentations covering innovative approaches to viral hepatitis, cytomegalovirus (CMV), Epstein-Barr virus, human herpesvirus-8, BK polyomavirus, infectious encephalitis, and vaccination strategies. Particular emphasis was placed on the growing role of metagenomic next-generation sequencing for diagnosing unexplained infections, the integration of immune monitoring into clinical decision-making, and the development of adoptive cellular therapies, including virus-specific αβ T cells and γδ T-cell-based immunotherapies for refractory CMV infection. The meeting also highlighted emerging concepts in donor-recipient immunogenetics, novel diagnostic technologies, and personalized preventive strategies. Collectively, these advances illustrate the transition toward precision medicine in transplant infectious diseases, combining cutting-edge diagnostics, immune profiling, and innovative immunotherapeutic approaches to improve the management and outcomes of solid organ transplant recipients.},
}

Humans
*Organ Transplantation/adverse effects
*Virus Diseases/diagnosis/therapy
Antiviral Agents/therapeutic use

@article {pmid42638748,
year = {2026},
author = {Liu, W and Liu, J and Chen, Y and Lu, G and Shen, J and Zheng, X and Wei, X},
title = {Colorectal laterally spreading tumors exhibit a distinct carcinogenic eco-metabolic shift defined by multi-omics profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1887252},
pmid = {42638748},
issn = {1664-302X},
abstract = {BACKGROUND: Colorectal laterally spreading tumors (LSTs) are clinically important premalignant lesions with distinctive endoscopic morphology and malignant potential. Although microbiome and metabolome alterations have been reported in colorectal cancer and conventional adenomas, the microbial and metabolic features associated with LSTs remain insufficiently characterized.

OBJECTIVE: We investigated whether LSTs are associated with a coordinated carcinogenic eco-metabolic shift (CES) involving stool microbial, metagenomic functional, and circulating metabolic alterations, hereafter referred to a CES, a finding consistent with its high-risk premalignant biology.

METHODS: Building on our LST multi-omics cohort, we focused on stool metagenomic, serum metabolomic, and paired stool-serum datasets from 35 LST patients and 35 healthy controls. LST-associated microbial taxa, serum metabolites, and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional features were organized into CES modules according to their biological direction and functional themes. Cross-layer Spearman's analyses, functional pathway analyses, and sign-aligned CES scores were used to assess coordination across microbial, functional, and metabolic layers. Publicly available MetaGenoPolis stool metagenomic data were used as a reference cohort for comparisons across healthy controls, adenoma, and colorectal cancer (CRC) disease sequences.

RESULTS: LST patients showed a CES characterized by the depletion of protective anaerobe-associated taxa; enrichment of facultative/pathobiont-associated taxa; remodeling of dicarboxylate/TCA axis metabolism; alterations in amino acid and choline/glycerophospholipid metabolism; and enrichment of microbial functions related to carbohydrate uptake, central carbon metabolism, transport, and biofilm-associated adaptation. In paired stool-serum samples, four cross-layer associations were retained, including an exploratory inverse Roseburia-succinate relationship. In the MetaGenoPolis cohort, the matched microbial component of the CES showed a CRC-oriented pattern: CRC patients had higher microbial CES scores than healthy controls and adenoma patients, whereas the microbial CES scores of healthy controls and adenoma patients were not significantly different. Sign-aligned CES scores were higher in LST patients than in healthy controls across stool, serum, and paired multi-omics analyses; the paired integrated CES score showed a rank-biserial effect size of 0.952. A compact five-anchor CES representation, based on Roseburia depletion, succinate elevation, phosphotransferase system (PTS) elevation, 3-hydroxybutyric acid depletion, and Escherichia enrichment, preserved the main signal.

CONCLUSION: LSTs are associated with a coordinated CES involving stool microbial, microbial functional, and serum metabolic alterations. These findings support the CES as a testable framework for understanding high-risk premalignant colorectal biology and warrant validation in larger cohorts with adenoma and serrated lesion comparators.},
}

@article {pmid42638844,
year = {2026},
author = {Zhang, X and Liu, H and He, C and Chen, H and Zhang, H and Li, F},
title = {Comparative metagenomic and untargeted metabolomic analyses reveal gut microbiota and metabolite alterations associated with diarrhea in neonatal Holstein calves in Anhui, China.},
journal = {Veterinary world},
volume = {19},
number = {7},
pages = {2763-2776},
pmid = {42638844},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Neonatal calf diarrhea remains a major cause of morbidity, mortality, and economic losses in the dairy industry. Although alterations in gut microbial communities have been implicated in calf diarrhea, the interactions between intestinal microbiota and metabolites in neonatal Holstein calves remain incompletely understood. This study aimed to characterize gut microbiome and metabolomic alterations associated with diarrhea and to explore the relationships between differential microorganisms and metabolites in neonatal Holstein calves from Anhui, China.

MATERIALS AND METHODS: Fecal samples were collected from four diarrheic and four healthy female Holstein calves younger than 2 weeks of age. Shotgun metagenomic sequencing was performed using the DNBSEQ-T7 platform, and untargeted liquid chromatography-tandem mass spectrometry metabolomics was used to characterize fecal metabolites. Multivariate analyses, biomarker identification, pathway enrichment, and correlation analyses were conducted to investigate associations between microbial taxa and metabolites.

RESULTS: Distinct microbial and metabolic profiles were observed between healthy and diarrheic calves. Analysis of similarities confirmed significant differences in microbial composition between groups (R = 0.7917, p = 0.025). Forty microbial biomarkers were identified, with Campylobacter jejuni, Campylobacter coli, and Bacillus cereus showing increased abundance in diarrheic calves, whereas beneficial taxa such as Faecalibacterium prausnitzii were enriched in healthy calves. Metabolomic analysis identified 377 differential metabolites, including 130 upregulated and 247 downregulated compounds in diarrheic calves. Pathway analysis indicated that D-glutamine and D-glutamate metabolism was the most affected pathway, together with alanine, aspartate, and glutamate metabolism, thiamine metabolism, taurine and hypotaurine metabolism, and cysteine and methionine metabolism. Five key metabolites, glutamate, α-ketoglutaric acid, thiamine, 3-sulfinoalanine, and S-adenosyl-L-homocysteine, were strongly associated with differentially abundant microorganisms. Correlation analyses demonstrated significant microbe-metabolite interactions, suggesting that dysbiosis contributes to metabolic disturbances during diarrhea.

CONCLUSION: Neonatal calf diarrhea was associated with pronounced alterations in gut microbial communities and fecal metabolites. The enrichment of opportunistic pathogens and disruption of amino acid-related metabolic pathways highlight potential biomarkers and mechanistic links underlying gut dysbiosis. These findings provide novel insights into microbiota-metabolite interactions and may facilitate the development of targeted strategies to improve calf health and reduce economic losses in dairy production.},
}

@article {pmid42639016,
year = {2026},
author = {Lyu, T and Gao, S and Wang, W and Liu, W},
title = {Severe ARDS caused by Strongyloides stercoralis hyperinfection in a patient with Sjögren's syndrome: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1892861},
pmid = {42639016},
issn = {2296-858X},
abstract = {BACKGROUND: Strongyloides stercoralis (S. stercoralis) is a neglected tropical disease that can be fatal in immunocompromised hosts. Diagnosis is challenging due to nonspecific clinical manifestations and low sensitivity of conventional stool examination. Patients with autoimmune diseases receiving long-term glucocorticoid therapy are at high risk of hyperinfection syndrome, which can rapidly progress to acute respiratory distress syndrome (ARDS).

CASE PRESENTATION: A 65-year-old man with an 8-year history of Sjögren's syndrome and chronic interstitial lung disease, who had been on long-term oral methylprednisolone, tripterygium glycosides, and hydroxychloroquine, presented with abdominal pain and vomiting. He rapidly developed severe ARDS requiring invasive mechanical ventilation. Laboratory tests showed persistent eosinopenia (0.01 × 10[9]/L) and lymphopenia. Bronchoalveolar lavage fluid was subjected to metagenomic capture sequencing (MetaCAP), which revealed S. stercoralis [16,030 reads per million (RPM)] and cytomegalovirus (14,397RPM). Sputum smear microscopy showed motile S. stercoralis larvae, confirming the diagnosis. The patient was treated with albendazole (0.4 g via nasogastric tube twice daily) combined with ivermectin (12 mg via nasogastric tube once daily) for strongyloidiasis, together with ganciclovir for cytomegalovirus. Because of severe ARDS and possible autoimmune flare, methylprednisolone (80 mg intravenously every 12 h followed by tapering) was cautiously administered under effective anti-infective coverage. Two days after treatment, the oxygenation index improved from 77 mmHg to 214 mmHg. One week later, repeat MetaCAP showed a marked reduction of S. stercoralis reads to 69RPM and cytomegalovirus 9 RPM. The patient was successfully extubated and discharged after consolidation therapy. At nine-month follow-up he remained well.

CONCLUSION: This case demonstrates that S. stercoralis hyperinfection can occur without eosinophilia in immunocompromised patients with autoimmune diseases and can rapidly progress to ARDS. MetaCAP of bronchoalveolar lavage fluid enables rapid and sensitive diagnosis. Short-term glucocorticoid therapy to control ARDS and autoimmune disease activity is feasible and safe provided that effective anti-infective treatment is in place.},
}

@article {pmid42639087,
year = {2026},
author = {Li, N and Hu, J and Tong, W and Liu, C and Ding, Y and Li, N and Cai, Z},
title = {LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1906036},
pmid = {42639087},
issn = {2673-7647},
abstract = {INTRODUCTION: Bronchoalveolar lavage fluid metagenomic next-generation sequencing captures microbial profiles and host-derived molecular measurements from the same respiratory specimen, but downstream analysis requires coordinated handling of low-biomass microbial signals, negative-control information and multiple feature tables.

METHODS: We developed LungMicroHostR, an R package for downstream host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data. The package brings processed microbial profiles, host-derived molecular measurements, sample metadata and negative-control information into a unified R workflow for feature filtering, comparative model evaluation, visualization and reproducible reporting.

RESULTS: Using the public GSE252118 resource comprising 402 samples from patients with lung cancer or pulmonary infections, LungMicroHostR assembled matched microbial, host and clinical feature tables, estimated prevalence in negative controls and compared host transcriptomic, microbial-profile and combined host-microbial models. In the test set, the 10-feature host transcriptome nearest-centroid model achieved an AUC of 0.772 (95% confidence interval, 0.680-0.860), the five-feature RNA microbial logistic model achieved an AUC of 0.745 (0.655-0.832), and the combined host transcriptome-RNA microbial logistic model achieved an AUC of 0.765 (0.655-0.866) with balanced accuracy of 0.720. An external PRJNA714488 BALF shotgun metagenomic dataset was additionally analysed at the mOTU level; LungMicroHostR matched the resulting feature table with phenotype metadata and generated a 388-feature by 26-sample microbial abundance matrix.

DISCUSSION: LungMicroHostR provides documented functions for respiratory metagenomic analyses that require joint evaluation of microbial profiles, host-derived measurements, negative-control information and external microbial feature tables.},
}

@article {pmid42639172,
year = {2026},
author = {Chen, J and Guan, Y and Li, W and Bao, Y and Wang, Z and Sun, Z and Hu, X and Jiang, H},
title = {Metagenomic Characterization of Nitrite-Negative Urinary Tract Infections and Identification of an optrA-fexA Co-Localization in a Primary Healthcare Setting in China.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {605077},
pmid = {42639172},
issn = {1178-6973},
abstract = {INTRODUCTION: Urinary tract infections (UTIs) showing negative nitrite results create a diagnostic blind spot for Gram-positive pathogens. The plasmid-mediated resistance genes optrA (linezolid) and tet(X) (tigecycline) pose severe therapeutic challenges, but their genomic context in primary healthcare settings remains poorly characterized.

METHODS: Deep metagenomic sequencing was performed on urine samples from 20 patients with complex nitrite-negative UTIs and pyuria in China. Antibiotic resistance genes (ARGs) were profiled using a read-mapping threshold (>50 reads for tet(X)) and de novo assembly.

RESULTS: optrA was ubiquitously detected via read mapping. Based on our pre-established cutoff, tet(X) reads were identified in 55% (11/20) of samples. Crucially, genomic assembly captured the physical co-localization of optrA and the phenicol exporter fexA on a single contig in one sample (JX-NY001). Virulence factor profiles varied across samples.

DISCUSSION: This study provides genomic evidence of high-risk resistance determinants in community nitrite-negative UTIs. However, results are limited by the DNA-level metagenomic approach without culture confirmation. Molecular surveillance is needed to monitor these cryptic multidrug-resistance clusters.},
}

@article {pmid42639329,
year = {2026},
author = {Li, W and Zhao, M and Wu, W and Chen, G and Hang, Y and Zheng, H and Gao, Z and Liu, J and Zhao, Y},
title = {Correction: The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1949477},
doi = {10.3389/fcimb.2026.1949477},
pmid = {42639329},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1494638.].},
}

@article {pmid42639503,
year = {2026},
author = {Dede, B and Zehnle, H and Skoog, E and Priest, T and Beck, K and Bürgmann, H and Schoelmerich, MC},
title = {Active microbial communities and their extrachromosomal elements link organic matter degradation to methane cycling in anoxic sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag217},
pmid = {42639503},
issn = {2730-6151},
abstract = {Anaerobic carbon transformation in freshwater sediments drives substantial methane emissions globally, yet the microbial taxa linking complex carbon degradation to methane production remain poorly characterized. Here, we combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno (Swiss Alps) to identify the active microbial clades, metabolic pathways, and extrachromosomal elements (ecDNA) across a depth gradient within the upper 56 cm of sediment. We recovered 802 species-level metagenome-assembled genomes spanning 66 phyla and identified a Bacteroidota clade (VadinHA17) as one of the most abundant and transcriptionally active populations in the sediment. This clade encodes and transcribes a broad range of diverse glycoside hydrolases (GH), indicating a central role in complex carbohydrate degradation. Transcriptional profiles suggest that this clade ferments organic substrates to acetate and hydrogen, which are key substrates for methanogenesis. In line with this, the acetoclastic methanogen Methanothrix and hydrogenotrophic Methanoregula were among the most abundant and transcriptionally active archaea in the same depth layers as VadinHA17. Beyond microbial genomes, we detected 86 905 viral OTUs and 2136 plasmid OTUs, with free viruses and plasmids accounting for 5%-10% and 0.2% of all sequencing reads, respectively. Notably, plasmids and viruses associated with Bacteroidota VadinHA17 encode and transcribe GHs that could augment host carbohydrate-degrading capacity. Together, these findings reveal new details on how methane production in anoxic lake sediments emerges from a network spanning primary fermentation, methanogenesis, and ecDNA-mediated metabolisms.},
}

@article {pmid42640096,
year = {2026},
author = {Rolando, JL and Krueger, GM and Duchesneau, K and Kostka, JE},
title = {Metagenome-assembled genomes from Spartina alterniflora salt marsh roots and sediments along the U.S. Atlantic coast.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0079126},
doi = {10.1128/mra.00791-26},
pmid = {42640096},
issn = {2576-098X},
abstract = {Spartina alterniflora is the dominant plant in low-elevation salt marshes along the U.S. Atlantic coast. Here, we present 434 metagenome-assembled genomes assembled from 36 metagenomic libraries of S. alterniflora sediment and root samples in Georgia, Virginia, and Massachusetts. Samples were collected across natural environmental stress gradients at all sites.},
}

@article {pmid42640098,
year = {2026},
author = {Slater, D and Kar, S and Worby, CJ and Crowley, J and Kawser, Z and Shamsuzzaman, SM and Harding, C and Earl, AM and LaRocque, R and Qadri, F and Harris, J},
title = {High exposure, rapid turnover: strain-level dynamics of Klebsiella pneumoniae carriage in community and hospitalized populations in Bangladesh.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0165126},
doi = {10.1128/spectrum.01651-26},
pmid = {42640098},
issn = {2165-0497},
abstract = {The gastrointestinal (GI) tract serves as a reservoir of Klebsiella pneumoniae (Kp), facilitating transmission of invasive strains and dissemination of antimicrobial resistance genes (ARG). Studies of drug-resistant strains in hospitalized patients, during care, and post-discharge, have shown that Kp may persist for months to years in the GI tract. In contrast, there are limited longitudinal data characterizing the duration of Kp GI carriage in healthy populations. In this study, we evaluated a previously described population from an urban neighborhood of Dhaka, Bangladesh, using metagenomic analyses of Kp-enriched fecal cultures to characterize strain-level and ARG carriage dynamics over a 2-month period, and we compared this with Kp carriage data from a contemporaneously enrolled hospitalized cohort from Dhaka Medical College Hospital. Our results show high rates of Kp carriage in both groups, along with frequent co-carriage of multiple drug-resistant strains. Overall, Kp strains were genetically diverse, and carriage of individual strains was typically short-lived, with extensive turnover between time points. We also observed age-associated increases in IgG antibody responses to common Kp surface antigens, which we postulate reflect the effect of repeated, frequent exposures to Kp in these populations. Together, these findings provide insights into the carriage dynamics of Kp in a highly endemic setting.IMPORTANCEKlebsiella pneumoniae is a leading cause of antibiotic-resistant healthcare-associated infections, with the World Health Organization listing carbapenem-resistant strains as a priority pathogen. Gastrointestinal (GI) carriage is recognized as a risk factor for invasive disease in hospitalized patients, with the infecting strain often originating from the patient's own gut microbiota. Less is known about non-hospitalized populations, where GI carriage is common but asymptomatic. By defining strain-level dynamics and characterizing the antimicrobial resistance genes (ARGs) circulating in a highly endemic community, this study provides a valuable counterpoint to previous research focused on hospital settings and contributes to our understanding of the diversity and dynamics of circulating strains in healthy populations where the burden of Klebsiella pneumoniae is high.},
}

@article {pmid42640339,
year = {2026},
author = {Li, J and Zhang, Y and Yang, K and Yang, Y and Chang, Z and Xu, T and Song, F and Chang, W},
title = {Arbuscular mycorrhizal fungi reshape rhizosphere microbial communities to alleviate phosphorus deficiency in soda-saline soils.},
journal = {Mycorrhiza},
volume = {36},
number = {5},
pages = {},
pmid = {42640339},
issn = {1432-1890},
support = {No. 32571883//The National Natural Science Foundation of China/ ; No. LH2024C091//Natural Science Foundation (Joint Guidance) of Heilongjiang Province/ ; No. 2025-KYYWF-ZR0407//Basic Scientific Research Business Expenses for Provincial Universities of Heilongjiang Province/ ; },
mesh = {*Mycorrhizae/physiology ; *Rhizosphere ; *Phosphorus/metabolism/deficiency ; *Soil Microbiology ; *Soil/chemistry ; Bacteria/metabolism/classification ; *Microbiota/physiology ; },
abstract = {Phosphorus availability is severely constrained in soda saline-alkali soils; yet the mechanisms by which arbuscular mycorrhizal (AM) fungi modulate rhizosphere microbial communities to alleviate the limitation are still unresolved. In the research, a microcosm experiment is conducted with metagenomic sequencing to investigate how inoculation with Rhizophagus intraradices influenced rhizosphere properties, phosphorus fractions, phosphatase activities, microbial community structure, P-cycling gene networks, and growth of Elaeagnus angustifolia under soda saline-alkali stress. The results demonstrated that AM inoculation was associated with enhanced plant growth and root development, ameliorated rhizosphere physicochemical conditions, elevated phosphatase activities, and enrichment of organic phosphorus-mineralizing bacteria, primarily Actinobacteria (Streptomyces) and Proteobacteria (Pseudoxanthomonas, Sphingomonas, Variovorax). Critically, the P-cycling gene network was reorganized, with hubs shifting from inorganic phosphorus transport genes toward organic phosphorus mineralization genes. Variance partitioning analysis further indicated that AM fungi independently contributed to variation in P-cycling functional genes, whereas their influence on soil phosphorus pools and phosphatase activity appeared to be largely indirect and associated with changes in soil chemical properties. Collectively, these findings support the hypothesis that AM fungi may promote phosphorus mobilization and transfer toward plants by restructuring microbial community composition and functional potential, providing a foundation for microbial management strategies in soda saline-alkali soils.},
}

*Mycorrhizae/physiology
*Rhizosphere
*Phosphorus/metabolism/deficiency
*Soil Microbiology
*Soil/chemistry
Bacteria/metabolism/classification
*Microbiota/physiology

@article {pmid42640403,
year = {2026},
author = {Parveen, S and Tak, H and Ganai, BA and Aien, Q and Wana, GM and Kousar, A},
title = {Host-parasite-microbiome interactions in gastrointestinal trematodes and cestodes of small ruminants: current advances and future perspectives.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42640403},
issn = {1573-7446},
support = {23D/23J00547//Human Resource Development Centre, Council of Scientific And Industrial Research/ ; },
mesh = {Animals ; *Trematoda/physiology ; *Cestoda/physiology ; *Host-Parasite Interactions ; *Trematode Infections/veterinary/parasitology ; *Cestode Infections/veterinary/parasitology ; Sheep ; Goats ; *Goat Diseases/parasitology/microbiology ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; Rumen/parasitology/microbiology ; Ruminants/parasitology ; },
abstract = {Gastrointestinal helminth infections remain a major problem for sheep and goat farming worldwide. In the past, research mainly focused on the shape, classification, spread, health effects, and genetic makeup of the parasites. With the advent of new next-generation sequencing technologies, we now better understand the gut ecosystem and the important roles of host-parasite-microbiome interactions in animal health. The digestive tract of sheep and goats contains microbes that aid digestion, nutrient utilization, immune function, and the maintenance of homeostasis. New research shows that helminths can change these microbial communities by affecting the immune system, damaging tissues, and competing for nutrients. At the same time, the existing microbes can affect how parasites settle, survive, and cause disease. Unlike studies on other parasites, research on the microbiomes of rumen flukes (Paramphistomum, Cotylophoron, and Calicophoron) and cestodes (Moniezia, Avitellina, and Stilesia) remains very limited, despite these parasites inhabiting environments rich in microbes, such as the rumen and small intestine. This review brings together what is currently known about the diversity, distribution, preferred habitats, and interactions among hosts, parasites, and microbiomes of gastrointestinal trematodes and cestodes in small ruminants. It focuses on metagenomic methods, the microbiota linked to these parasites, and new possibilities for microbiome research. The review also highlights important gaps in our knowledge and emphasizes the need for combined morphological, molecular, and next-generation sequencing studies, especially in areas such as Kashmir, where these parasites are common. Learning more about the microbes associated with these helminths could offer new insights into parasite biology and help develop better ways to diagnose, monitor, and control infections, supporting more sustainable small-ruminant farming.},
}

Animals
*Trematoda/physiology
*Cestoda/physiology
*Host-Parasite Interactions
*Trematode Infections/veterinary/parasitology
*Cestode Infections/veterinary/parasitology
Sheep
Goats
*Goat Diseases/parasitology/microbiology
*Sheep Diseases/parasitology/microbiology
*Gastrointestinal Microbiome
Rumen/parasitology/microbiology
Ruminants/parasitology

@article {pmid42640703,
year = {2026},
author = {Lewandowski, R},
title = {Emergent function, not microbial conformity: functional redundancy and the limits of taxonomic inference in microbiome genomics.},
journal = {Microbial genomics},
volume = {12},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001831},
pmid = {42640703},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Genomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification ; Host Microbial Interactions ; },
abstract = {Microbiome genomics has achieved remarkable resolution of community structure, yet composition alone remains an unstable basis for inferring host-relevant biology. That instability reflects a broader interpretive problem in which taxonomically distinct communities can converge on similar outputs, while superficially similar communities can diverge in behaviour because of strain variation, gene content, regulatory state, ecological context, spatial organization and host physiology. Functional redundancy is therefore better understood not as a reserve of interchangeable organisms but as a distributed functional architecture through which host-relevant outputs can persist across variation in membership. The central question for microbial genomics is not whether composition matters, but when community structure can be expected to predict function, host consequence or recovery. A more rigorous framework must distinguish membership from encoded capacity, realized activity, ecological interaction and host-relevant effect, while also recognizing that host physiology and spatial context shape which microbial functions become possible and which outputs are ultimately encountered. Progress will depend first on matching the evidentiary layer to the claim and then on selecting proportionate additions, from strain-resolved genomics and pathway-level interpretation to targeted metatranscriptomic, metaproteomic, metabolomic, spatial, perturbation-recovery or host-response measurements. In that framework, reproducibility may reside less in recurring taxa than in conserved biological outputs, and restoration less in compositional resemblance than in recovery of the functions and host-facing consequences that were actually disrupted.},
}

*Microbiota/genetics
*Genomics/methods
*Metagenomics/methods
*Bacteria/genetics/classification
Host Microbial Interactions

@article {pmid42640706,
year = {2026},
author = {Whelan, FJ and Hall, LJ},
title = {An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.},
journal = {Microbial genomics},
volume = {12},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001823},
pmid = {42640706},
issn = {2057-5858},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Metagenomics/methods ; Humans ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The 16S rRNA gene has - and continues to - play an important role in microbiology. It's universality across prokaryotes and variation across species has allowed the sequencing of its hypervariable regions to be used to distinguish taxa within complex mixed bacterial communities. Although 16S rRNA gene sequencing has transformed our understanding of microbial communities, its use comes with important caveats and considerations, especially in light of the availability of whole-genome metagenomic sequencing. Within, we discuss the 16S rRNA gene and its important role in microbiome research, in the past, present, and future.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/classification
Metagenomics/methods
Humans
Phylogeny
Sequence Analysis, DNA

@article {pmid42640826,
year = {2026},
author = {Alvarez Saravia, D and Rosenbaum, A and Straub, D and Downie, J and Borry, M and Fedewa, G and H Ubner, A and Lundin, D and Yepes-Garćıa, J and McDonald, J and Nahnsen, S and K Ohn, L and Uribe-Paredes, R and Navarrete, MA and Warinner, C and , and Fellows Yates, JA},
title = {Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag628},
pmid = {42640826},
issn = {1367-4811},
abstract = {SUMMARY: nf-core/mag is a reproducible Nextflow pipeline for best-practice metagenomic de novo assembly, and binning within the nf-core framework. Here we present a major update that adds support for long-read-only assembly and bin refinement, includes five new binning tools, expands taxonomic classification to viruses and eukaryotes, and improves bin quality evaluation with new tools and latest databases. Through sustained community-driven development spanning seven years and four primary curator teams, nf-core/mag remains actively developed as an open-source workflow for metagenomic analysis, benefiting from contributions from across the broader metagenomics, nf-core, and Nextflow ecosystem.

The source code of nf-core/mag v5 is available on GitHub (https://github.com/nf-core/mag) under the open source MIT license, with v5.5.0 source code archived on Zenodo (https://zenodo.org/records/21735731). Documentation is viewable on the nf-core website (https://nf-co.re/mag).

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