@article {pmid41499025,
year = {2026},
author = {Cunanan, DJ and Carandang, THDC and Pilapil, JD and Cunanan, DJ and Mollasgo, AG and Manalo, GNS and Co, GS and Rosch, J and Carroll, K and Notarte, KI},
title = {Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {45},
number = {4},
pages = {1077-1091},
pmid = {41499025},
issn = {1435-4373},
abstract = {PURPOSE: Accurate and timely diagnosis is essential to ensure effective management of bacterial pneumonia to improve patient outcomes. This study aims to evaluate the use of metagenomic nanopore sequencing in the microbiological diagnosis of pneumonia compared to standard diagnostic procedures. METHODS: A comprehensive literature search across multiple databases was performed. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy 2 (QUADAS-2) tool. Pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and area under the curve (AUC) were determined. RESULTS: Thirteen studies were included in the systematic review, with eight eligible for meta-analysis. In the microbiological diagnosis of bacterial pneumonia, the overall sensitivity of nanopore sequencing using both MinION and GridION platforms is 86.08% (95% CI 75.96–92.37) while specificity is 84.97% (95% CI 75.94–91.02). Results show a high PPV (85.13%; 95% CI 77.72–90.38) and high NPV (85.27%; 95% CI 76.79–91.01). Nanopore sequencing also has a high diagnostic value based on the computed AUC (0.922) and DOR (40.68; 95% CI 11.22–147.48). Sensitivity analyses suggest a trend toward higher diagnostic accuracy for bacterial pneumonia with the MinION device and lower accuracy with the GridION platform. We also found that accuracy is higher when the focus of diagnosis is ventilator-associated pneumonia (VAP) and when endotracheal aspirate alone is utilized as the sample type. CONCLUSIONS: Nanopore sequencing offers faster, real-time results compared to traditional culture. It also shows higher specificity than short-read metagenomic next-generation sequencing (mNGS), particularly in ventilator-associated pneumonia. Further research is warranted for subgroup analyses to optimize the use of nanopore sequencing in detecting bacterial pneumonia.},
}

@article {pmid41511674,
year = {2026},
author = {Yin, Q and Mei, X and Ma, Y and Zheng, M},
title = {Central nervous system infections caused by carbapenem-resistant klebsiella pneumoniae after CAR T-cell therapy in a patient with preexisting colonization: a case report and literature review.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {45},
number = {5},
pages = {1491-1499},
pmid = {41511674},
issn = {1435-4373},
support = {81974005//National Natural Science Foundation of China/ ; Y-SYBLD2022MS-0055//the Beijing Xisike Clinical Oncology Research Foundation/ ; 2025AFD777//the Joint Fund for Innovation and Development of Natural 205 Science Foundation of Hubei Province/ ; },
abstract = {OBJECTIVE: To investigate the risk factors for corresponding infections following chimeric antigen receptor (CAR) T-cell infusion in Carbapenem-resistant Enterobacteriaceae (CRE) carriers and to provide insights for managing such cases. METHODS: A retrospective analysis was performed on the clinical presentation, laboratory findings, treatment, and prognosis of a patient with preexisting colonization who developed CRE intracranial infection after CAR T-cell therapy. A systematic review of the literature was conducted to explore optimal antibiotic strategies for CRE-associated central nervous system infections. RESULTS: Carbapenem-resistant Klebsiella pneumoniae was detected in perianal swabs before preconditioning chemotherapy, and the patient subsequently received high-dose corticosteroids for cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome following CAR T-cell infusion. Despite broad-spectrum coverage, recurrent fevers and convulsions ensued. Metagenomic next-generation sequencing of cerebrospinal fluid on day +14 confirmed Kbsiella pneumoniae infection, later identified as a multidrug-resistant strain. Clinical and microbiological clearance was achieved following combination therapy centered on intravenous ceftazidime-avibactam, supplemented with intrathecal polymyxin B, guided by antibiotic susceptibility testing. The patient ultimately died three months later due to lymphoma progression. CONCLUSION: Defining optimal management strategies for CRE carriers is essential to integrate infection risk mitigation into the personalized framework of CAR T-cell therapy.},
}

@article {pmid41654923,
year = {2026},
author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY},
title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41654923},
issn = {1479-5876},
support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.},
}

@article {pmid41779333,
year = {2026},
author = {Hu, Y and Li, A and Qiu, S and Zhu, T and Guo, J and Zhang, W and Zhao, C and Lyu, Y},
title = {Characteristics of Multispecies Bacterial Cocultures for the Removal of Ammonia, Nitrate, and Nitrite from Water.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {5},
pages = {3811-3830},
pmid = {41779333},
issn = {1559-0291},
support = {2025AFD305//Hubei Provincial Natural Science Foundation - Yichang Innovation and Development Joint Fund/ ; },
abstract = {The removal of ammonia, nitrate, and nitrite from wastewater is essential for controlling nitrogen pollution. However, the efficiency of biological nitrogen removal is often limited by the scarcity of highly active bacterial strains. In this study, a coculture system, designated YEM003, was constructed using eight nitrogen-metabolizing bacterial strains isolated from the same activated sludge. YEM003 exhibited robust nitrogen removal performance, effectively eliminating ammonia, nitrate, and nitrite from wastewater under varying oxygen conditions. Metagenomic analysis revealed enrichment of key genes involved in nitrogen metabolism and elucidated nitrogen removal pathways of YEM003. Due to the unbalanced abundance distribution of the eight strains in YEM003, the contributions of each strain to the nitrogen removal metabolism in different wastewaters differed significantly. Overall, YEM003 exhibits comprehensive and efficient biological nitrogen removal capabilities and shows strong potential for application in wastewater nitrogen removal processes.},
}

@article {pmid41803286,
year = {2026},
author = {Zhu, C and Zhu, Y and Gao, H and Wang, X and Guo, Y and Sun, H and Qi, M and Zhang, B and Hu, Y},
title = {Long-Term Preservation of Humid Earthen Sites: Shelter Efficacy, Essential Oil Dynamics, and Microbial Adaptation.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41803286},
issn = {1432-0991},
support = {2023C03G1752302//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {This study evaluates the long-term conservation of humid earthen archaeological sites using protective shelters and plant essential oil treatments at the Laohuling Dam (Liangzhu, China), a UNESCO World Heritage site. Over seven years (2017–2024), structural deterioration, biological colonization, and microbial community dynamics were monitored through field surveys, amplicon sequencing (16 S rRNA and ITS), and shotgun metagenomics. Protective shelters effectively reduced large-scale structural damage and higher-plant colonization; however, enclosed and climate-controlled conditions promoted persistent microbial biofilms in high-humidity zones. Oregano essential oil treatments rapidly eliminated visible biofilms and suppressed recolonization for approximately 6–8 months, but did not prevent long-term microbial recovery. Post-treatment communities shifted from phototrophic and biofilm-forming taxa toward fast-growing, opportunistic heterotrophs, predominantly affiliated with Pseudomonadota. Metagenomic analyses revealed a stable resistome across consecutive treatment years. The high abundance of multidrug resistance genes (e.g., adeF, β-lactam- and CAMP-associated genes) primarily reflected the dominance of Pseudomonadota-related taxa rather than evidence of resistance evolution driven by essential oil application. No significant increase in resistance gene diversity or abundance was detected. These findings demonstrate that sheltering and essential oil treatments are effective short-term conservation tools but reshape microbial succession rather than eliminating biological risks. Long-term preservation of humid earthen sites therefore requires integrated strategies combining microclimate control, low-bioreceptivity materials, and continuous microbial monitoring.},
}

@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47816-9},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.},
}

@article {pmid42029951,
year = {2026},
author = {Kallistova, A and Savvichev, A and Toshchakov, S and Tutubalina, N and Rusanov, I and Petrova, K and Kadnikov, V and Beletsky, A and Zakharova, E and Ravin, N and Pimenov, N},
title = {Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42029951},
issn = {1432-0991},
support = {22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; },
abstract = {It is evident that climate change is causing glaciers to melt at an accelerated rate. This has a noticeable impact on the hydrological regime of high-altitude lakes, as well as the activity of microbial communities. However, the impact of climate change on microbial processes, abundance and diversity of microbial communities in high-altitude lakes remains to be elucidated. The objective of the study was to evaluate the structure, activity and metabolic capacity of microbial communities inhabiting the high-altitude Caucasus lake. Analytical and radiotracer methods were used together with 16S rRNA profiling, and metagenome analyses. Elevated concentrations of dissolved organic carbon (DOC) were observed in both the water column of the lake (12.2–19.4 mg/l) and the pore water of the sediments (6.3–15.8 mg/l). The intensity of photosynthesis in water column was very low. The bulk of phototrophs concentrated on the sediment surface where we suggest they produce organic matter due to sufficient light penetration and warming of the overlying water. The elevated DOC concentrations facilitated the activity of diverse heterotrophic microorganisms, resulting in oxygen depletion and activation of anaerobic processes in sediments. In case of an increase in the average annual temperature of the region, it is possible to predict the transformation of the lake into a eutrophic meromictic reservoir with constantly anoxic water layers, where sulfate reduction and methanogenesis would assume a pivotal role.},
}

@article {pmid42047869,
year = {2026},
author = {Gloanec, N and Huré, M and Bailly, L and Petit, É and Loutelier-Bourhis, C and Goux, D and Coëffier, M and Ribet, D},
title = {Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42047869},
issn = {1432-0991},
support = {SUMONING ANR-22-CE14-0064-01//Agence Nationale de la Recherche/ ; Labex SynOrg ANR-11-LABX-0029//Agence Nationale de la Recherche/ ; ANR-18-EURE-0020 XL CHEM//Agence Nationale de la Recherche (FR)/ ; },
abstract = {Isolating bacteria from the human gut microbiota and analyzing their phenotypes is essential for complementing the data obtained by metagenomics and for characterizing the functions of these microorganisms in human physiology. In this study, we isolated bacteria from the gut microbiota of healthy individuals and identified an uncharacterized bacterial strain that we designated HC1M1C21T. Phylogenetic analyses based on 16S rRNA and whole genome sequences indicated that this strain belongs to the family Lachnospiraceae. The closest relative of strain HC1M1C21T is Pilosibacter fragilis CSJ-4T (97.0% 16S rRNA gene sequence identity). P. fragilis was initially classified in the family Clostridiaceae. Based on our phylogenetic analyses, we propose to transfer the genus Pilosibacter from the family Clostridiaceae to the family Lachnospiraceae. HC1M1C21T has a DNA G + C content of 48.7%. This strain is anaerobic, Gram-stain-positive, non-motile and non-spore-forming. HC1M1C21T cells appear as single rods or chained rods with tapered ends. Optimal growth was observed at 37°C, at pH between 5.7 and 7.0 and at salinity below 10 g/L. HC1M1C21T is a potent butyrate producer. On the basis of these data, HC1M1C21T represents a novel species from the genus Pilosibacter, for which the name Pilosibacter rotomagensis sp. nov. is proposed. The type strain of P. rotomagensis is HC1M1C21T (= DSM 119410T=LMG 33828T).},
}

@article {pmid42062386,
year = {2026},
author = {Szklenarik, G and Dora, D and Szincsak, S and Acquah, CK and Biswas, A and Horváth, M and Galffy, G and Lohinai, Z},
title = {The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47296-x},
pmid = {42062386},
issn = {2045-2322},
abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic disorder affecting host–microbiome interactions beyond the airways. Although bacterial alterations in COPD have been documented, the gut mycobiome and its ecological integration with bacterial communities remain unexplored. In this study, we profiled the gut mycobiome of 61 non-small-cell lung cancer (NSCLC) patients stratified by COPD severity using ITS2 sequencing and analyzed 47 overlapping patients with available metagenomic data to construct cross-kingdom bacterial–fungal networks. Alpha diversity, assessed by Shannon, Simpson, and Chao1 indices, did not differ significantly between patients with and without severe COPD. Partial least squares discriminant analysis (PLS-DA) revealed partial separation of the two groups, with COPD severity explaining 6% of overall compositional variance (R[2]=0.06, p = 0.058). COPD-severe patients exhibited a significantly reduced Ascomycota/Basidiomycota ratio (p = 0.039) and lower relative abundance of Mucoromycota. Analysis of compositions of microbiomes (ANCOM) identified Myrothecium and Lasiodiplodia crassispora enriched in severe COPD, while Helotiales_unclassified and Phallus atrovolvatus were more abundant in non-severe cases. Fungal co-occurrence networks demonstrated reduced connectivity and modularity in severe COPD compared with non-severe COPD. Cross-kingdom analyses integrating bacterial genera revealed strengthened Candida–Enterococcus/Clostridium hubs and weakened Faecalibacterium/Roseburia–yeast associations in severe disease. Keystone analysis showed increased centrality for Candida, Aspergillus, Enterococcus, and Clostridium, and decreased centrality for Akkermansia and Roseburia. A compositional balance classifier achieved high discriminatory power (AUC = 0.88) in distinguishing COPD-severe from non-severe patients. These findings indicate that COPD severity is not characterized by major diversity loss but by guild-specific compositional shifts and extensive network rewiring, favoring oxygen-tolerant, opportunistic taxa over short-chain fatty acid–associated commensals.},
}

@article {pmid42343068,
year = {2026},
author = {He, G and Liu, T and Xing, J and Rao, L and Chen, S and Xie, C and Wei, G and Quan, X},
title = {In Situ Quorum Quenching Effect Induced by Negative Potential on Electro-Conductive Membranes for Membrane Fouling Control in Membrane Bioreactors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04557},
pmid = {42343068},
issn = {1520-5851},
abstract = {Membrane fouling is a major impediment to the widespread application of membrane bioreactors (MBRs) for water treatment. In recent years, the electro-conductive membrane bioreactor (E-MBR) has demonstrated efficacy in mitigating membrane fouling. The application of a negative potential to the electro-conductive membrane promotes electrostatic repulsion, effectively displacing negatively charged extracellular polymeric substances (EPS) away from the membrane surface. However, given the established vital role of quorum sensing (QS) in membrane fouling development, the interference of the negative potential on QS-mediated EPS secretion and biofilm formation has been largely overlooked. Herein, we found that the negative potential applied to the electro-conductive membrane could effectively suppress the QS process, thereby inducing the in situ quorum quenching (QQ) effect. The application of negative potential significantly reduced the levels of the signal molecule C14-HSL as well as EPS. Metagenomic analysis indicated that the relative abundance of the "signal transduction mechanism" pathway was suppressed, and the functional genes encoding C14-HSL receptor proteins belonging to "LuxR family" was downregulated in the cake layer of E-MBR. Density functional theory calculations and molecular dynamics simulation results revealed that the application of negative potential enhanced the electrostatic repulsion between the membrane and C14-HSL and induced the conformational changes of the LuxR protein, which synergistically induced the in situ QQ effect. This study provides a novel perspective on the antifouling mechanism in E-MBR.},
}

@article {pmid42343220,
year = {2026},
author = {Nichols, H and Molokin, A and Davies, CP and Maloney, JG},
title = {Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05298-9},
pmid = {42343220},
issn = {1471-2180},
support = {8042-32000-112-00-D//USDA, ARS/ ; },
abstract = {BACKGROUND: Microeukaryotic parasites of the intestinal tract are an understudied group of organisms that infect humans and many other animals. Targeted sequencing methods focused on individual loci are usually employed for detection of these parasites, making comprehensive studies of microeukaryotic parasite diversity within hosts or other systems difficult. Exploratory approaches such as shotgun metagenomic sequencing to survey the diversity of microeukaryotic parasites in new and existing datasets are not well developed.

RESULTS: Utilizing existing datasets from 12 goose fecal samples, we explored some of the benefits and challenges of using shotgun metagenome sequencing to detect microeukaryotic parasites. We demonstrated the importance of careful curation of read classification data to avoid erroneously linking pathogens to hosts or environments as unsupported classifications were common in the data and varied widely depending on analysis parameters. However, we were able to establish strong support for the presence of sequences of Eimeria and Enterocytozoon bieneusi. In addition, examination of trichomonad reads indicated that parasite reads mapping to human pathogens unlikely to colonize geese may in fact represent cryptic microeukaryotic species that are not included in existing curated databases opening new potential avenues of study.

CONCLUSIONS: Taken together these findings support the idea that exploring microeukaryotic parasite diversity within shotgun metagenomic datasets can be beneficial to our understanding of the presence and diversity of these organisms in wildlife hosts.},
}

@article {pmid42343233,
year = {2026},
author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM},
title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690689},
doi = {10.1080/19490976.2026.2690689},
pmid = {42343233},
issn = {1949-0984},
mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration & dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; },
abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.},
}

Humans
*Metabolic Syndrome/metabolism/microbiology/therapy
Female
Middle Aged
*Glucagon-Like Peptide 1/metabolism
Male
*Insulin Resistance
Double-Blind Method
*Probiotics/administration & dosage
*Body Composition
Adult
Akkermansia
*Verrucomicrobia
Gastrointestinal Microbiome
Pasteurization
Prediabetic State/metabolism
Aged

@article {pmid42343345,
year = {2026},
author = {Huang, H and Ye, X and Gu, D and Huang, E and Yu, X and Ai, L and Deng, J and Guo, P and Liu, H and Chen, Y and Wang, R and Luo, Y and Chen, P},
title = {Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03786-0},
pmid = {42343345},
issn = {1465-993X},
support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2022B1111020003//2021 Guangdong Province Key Areas Research and Development Plan "Biosafety Technology" Key Project/ ; 2023P-TS46//Featured Clinical Technique of Guangzhou/ ; 0720240122//Guangdong Provincial Center for Disease Control and Prevention Supports Talent Projects/ ; },
abstract = {BACKGROUND: Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) improves pathogen detection in severe pneumonia-related sepsis, but sampling is invasive and prone to false-positive results. Blood is easier to obtain, and broad-spectrum targeted NGS (tNGS) of microbial cell-free DNA may offer a practical alternative to BALF-based testing. We evaluated the diagnostic and prognostic value of blood-based bstNGS.

METHODS: In this retrospective cohort, 122 adults with suspected severe pneumonia-related sepsis and paired BALF and blood samples underwent BALF-mNGS, blood-bstNGS and blood-mNGS. Pathogens were adjudicated using a composite clinical reference. We assessed blood-BALF concordance, compared diagnostic performance across methods, and examined whether blood-bstNGS could down-weight likely false-positive BALF-only detections and stratify prognosis.

RESULTS: BALF-mNGS identified 414 microorganisms; 51% were adjudicated as causative or possibly causative, corresponding to 85.24% of patients. Among these pathogenic microorganisms, blood-bstNGS detected 45.02%, significantly more than blood-mNGS (22.27%), and nearly all pathogens detected by blood-mNGS were also detected by blood-bstNGS. Against the clinical reference, blood-bstNGS showed higher sensitivity (63.46%) than blood-mNGS (35.58%), conventional microbiological tests (CMTs) (49.04%), and blood culture (9.62%). Organisms detected only in BALF but not in blood were less likely to be classified as causative. Patients with concordant blood-bstNGS and BALF-mNGS profiles had significantly lower 30-day and 90-day mortality.

CONCLUSIONS: In severe pneumonia-related sepsis, blood-bstNGS provides sensitive, non-invasive pathogen detection. It acts as a complementary tool rather than a replacement for BALF-mNGS, offering an important diagnostic alternative when BALF is unavailable and improving specificity and prognostic utility when used in combination.},
}

@article {pmid42343457,
year = {2026},
author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X},
title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02453-2},
pmid = {42343457},
issn = {2049-2618},
abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.},
}

@article {pmid42343580,
year = {2026},
author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and L De Souza, M and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH},
title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.6c00391},
pmid = {42343580},
issn = {1520-6025},
abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and l-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.},
}

@article {pmid42343765,
year = {2026},
author = {Qiu, X and Lei, Z and Wang, J},
title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {5},
pages = {2103-2113},
doi = {10.13345/j.cjb.250783},
pmid = {42343765},
issn = {1872-2075},
support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; },
mesh = {*Solanum lycopersicum/growth & development/drug effects ; *Plant Roots/growth & development/drug effects ; *Seedlings/growth & development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; },
abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.},
}

*Solanum lycopersicum/growth & development/drug effects
*Plant Roots/growth & development/drug effects
*Seedlings/growth & development/drug effects
*Rhizosphere
*Soil Microbiology
*Graphite/pharmacology
*Microbiota/drug effects
Soil/chemistry
Nitrogen/metabolism

@article {pmid42343869,
year = {2026},
author = {Liang, P and Zhang, X and Cai, S and Hu, Z and Dong, L},
title = {Invasive aspergillosis in autoimmune inflammatory rheumatic diseases: epidemiology, risk factors, diagnosis, management and challenges.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2685285},
doi = {10.1080/07853890.2026.2685285},
pmid = {42343869},
issn = {1365-2060},
mesh = {Humans ; *Rheumatic Diseases/immunology/complications/drug therapy/epidemiology ; Risk Factors ; *Autoimmune Diseases/immunology/complications/drug therapy/epidemiology ; Aspergillus/immunology/isolation & purification ; Immunosuppressive Agents/adverse effects ; Immunocompromised Host ; *Opportunistic Infections/epidemiology/diagnosis/immunology ; Antifungal Agents/therapeutic use ; *Invasive Pulmonary Aspergillosis/epidemiology/diagnosis ; Aspergillosis/diagnosis/epidemiology ; },
abstract = {BACKGROUND: Invasive aspergillosis (IA) is a life-threatening opportunistic fungal infection caused by Aspergillus species. In recent years, IA appears to have become more frequently reported among patients with autoimmune inflammatory rheumatic diseases (AIIRD), likely reflecting the broader use of immunosuppressive therapies, with incidence in high-risk AIIRD subgroups reported to reach approximately 6.7% in selected cohorts.

OBJECTIVE: This review aims to summarize the current evidence on the epidemiology, susceptibility mechanisms, risk factors, clinical presentation, diagnosis, and management of IA in AIIRD, and to outline the clinical practical challenges in this population.

METHODS: This narrative review was informed by a structured literature search of PubMed, Embase, Web of Science, and Google Scholar for studies on IA in AIIRD published up to August 2025.

RESULTS: IA in AIIRD patients generally appears to arise from multiple interacting factors, including compromised host immunity, immunosuppressive therapy, the underlying rheumatic disease itself, comorbidities, and environmental exposures. Aspergillus infection and the resulting anti-Aspergillus immunity may also induce or exacerbate autoimmune inflammation. Invasive pulmonary aspergillosis is the most commonly reported manifestation, typically presenting with nonspecific respiratory symptoms, and disseminated infection tends to occur in the setting of profound immunosuppression. Early, integrated microbiologic testing (e.g. serum or bronchoalveolar lavage galactomannan, culture, polymerase chain reaction, and next-generation sequencing) together with serial imaging examination may facilitate earlier detection and guides care. Although robust AIIRD-specific evidence remains limited, current practice generally favour a multidisciplinary, individualized approach incorporating timely antifungal therapy and careful modulation of immunosuppression. Reported mortality remains high, ranging from 25% to 85% across AIIRD cohorts, particularly when diagnosis and treatment are delayed.

CONCLUSIONS: IA is a serious and likely under-recognized infection in AIIRD patients. Multiple determinants appear to increase infection risk, and symptoms and imaging manifestations can mimic rheumatic disease activity, potentially contributing to diagnostic delay. Current epidemiological and clinical data on AIIRD-IA remain limited, and further studies are needed to refine risk stratification, establish diagnostic criteria tailored to AIIRD patients, and inform more evidence-based management strategies.},
}

Humans
*Rheumatic Diseases/immunology/complications/drug therapy/epidemiology
Risk Factors
*Autoimmune Diseases/immunology/complications/drug therapy/epidemiology
Aspergillus/immunology/isolation & purification
Immunosuppressive Agents/adverse effects
Immunocompromised Host
*Opportunistic Infections/epidemiology/diagnosis/immunology
Antifungal Agents/therapeutic use
*Invasive Pulmonary Aspergillosis/epidemiology/diagnosis
Aspergillosis/diagnosis/epidemiology

@article {pmid42343917,
year = {2026},
author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T},
title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687219},
pmid = {42343917},
issn = {2000-2297},
abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.

RESULTS: Beta diversity demonstrated significant differences between groups (p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.},
}

@article {pmid42343927,
year = {2026},
author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD},
title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.},
journal = {Applications in plant sciences},
volume = {14},
number = {3},
pages = {e70064},
pmid = {42343927},
issn = {2168-0450},
abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.},
}

@article {pmid42343969,
year = {2026},
author = {Schaerer, LG and Anderson, RS and Chan, J and De Long, SK},
title = {Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag035},
pmid = {42343969},
issn = {2633-6685},
abstract = {Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/l to an average of 12.3 g/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. Lactiplantibacillus pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.},
}

@article {pmid42343970,
year = {2026},
author = {Das, R and Kumar, R and Tamang, B},
title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag032},
pmid = {42343970},
issn = {2633-6685},
abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.},
}

@article {pmid42343982,
year = {2026},
author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE},
title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.},
journal = {TH open : companion journal to thrombosis and haemostasis},
volume = {10},
number = {},
pages = {a28685248},
pmid = {42343982},
issn = {2512-9465},
abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.

OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.

METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known β2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.

RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell β2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-β2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-β2GP1 monoclonal antibody than a negative control.

CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.},
}

@article {pmid42344006,
year = {2026},
author = {Tepson, JA and Agyirifo, DS},
title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.},
journal = {International journal of food science},
volume = {2026},
number = {},
pages = {6618960},
pmid = {42344006},
issn = {2314-5765},
abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.},
}

@article {pmid42344497,
year = {2026},
author = {Yu, W and Yang, P and Ding, M and Guo, L and Liu, Y and Zhou, D and Gu, C},
title = {Acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with post-tuberculosis chronic pulmonary aspergillosis: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1828229},
pmid = {42344497},
issn = {2296-858X},
abstract = {This report describes a 59-year-old woman with a history of malignancy and post-tuberculosis lung disease complicated by chronic cavitary pulmonary aspergillosis. She was admitted with worsening hemoptysis and underwent bronchial artery embolization. However, she subsequently developed massive post-procedural hemoptysis, requiring mechanical ventilation. Sputum metagenomic next-generation sequencing detected SARS-CoV-2 and bacterial pathogens, prompting Paxlovid treatment for COVID-19 pneumonia. While her respiratory symptoms improved, epigastric pain developed. Based on elevated serum amylase/lipase and CT-confirmed peripancreatic inflammation, she was diagnosed with acute pancreatitis. One year later, pulmonary tuberculosis and liver metastasis recurred. This case highlights acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with multiple competing risk factors. Further, this case underscores the diagnostic complexity of structural lung disease with overlapping infections such as COVID-19 and stresses on the need for long-term surveillance.},
}

@article {pmid42344668,
year = {2026},
author = {Huang, F and Zhang, Z and Zhao, Y and Ye, S and Gan, M and Li, X and Zhang, Y and Chen, L and Zhang, Y and Chen, L and Wang, T and Huang, J and Zhang, X},
title = {Altitude-Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics.},
journal = {Evolutionary applications},
volume = {19},
number = {6},
pages = {e70285},
pmid = {42344668},
issn = {1752-4571},
abstract = {High-altitude environments expose mammals and their gut symbionts to multifaceted stressors-hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short-chain fatty acid (SCFA)-producing bacteria-centered on Flavonifractor plautii, Intestinimonas butyriciproducens, and Enterococcus faecium-that formed antagonistic co-occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high-altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch-specific regulation of the tryptophan-kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety-validated isolates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings provide an actionable framework for altitude-informed facility siting, fecal microbiota transplantation (FMT) donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome-associated disease pressure in captivity.},
}

@article {pmid42344740,
year = {2026},
author = {Zhang, X and Huo, H and Hu, L and Yang, F and Hu, X and Deng, Y and Feng, C and Wang, H and Huo, J},
title = {Dietary Lonicera japonica supplementation modulates cecal gut microbial composition and metabolomic profiles in weaned piglets.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1804735},
pmid = {42344740},
issn = {2297-1769},
abstract = {Weaning is a critical developmental stage in piglets and is often associated with intestinal dysbiosis, metabolic disturbances, and impaired gut barrier function. Phytogenic feed additives have emerged as promising natural alternatives to antibiotics for improving gut health. Lonicera japonica, a traditional medicinal and edible plant rich in bioactive compounds, exhibits well-documented antimicrobial, antioxidant, and immunomodulatory properties; however, its effects on the gut microbiota-metabolite axis in weaned piglets remain poorly understood. In this study, weaned piglets were fed either a basal diet (control group) or a Lonicera japonica-supplemented diet (experimental group). Cecal contents were collected for metagenomic sequencing to characterize gut microbial composition and for untargeted LC-MS-based metabolomic profiling. Functional pathway enrichment and microbe-metabolite correlation network analyses were conducted to elucidate potential mechanisms. Lonicera japonica supplementation significantly improved evenness in terms of microbial species richness and reshaped microbial community structure, characterized by the enrichment of beneficial taxa, including Firmicutes and Eubacterium coprostanoligenes, and a concomitant reduction in opportunistic pathogens such as Proteobacteria and Escherichia coli. KEGG pathway analysis revealed the upregulation of microbial pathways related to translation, replication, and energy metabolism, alongside the downregulation of stress-response-associated pathways. Metabolomic profiling demonstrated distinct metabolic signatures between groups, with elevated levels of unsaturated fatty acids, amino acid derivatives, and organic acids, and reduced bile acid intermediates in the Lonicera japonica-treated piglets. Correlation network analysis further revealed strong positive correlations between SCFA-producing bacteria and beneficial metabolites, underscoring a reinforced microbiota-metabolite axis. Collectively, these findings indicate that Lonicera japonica supplementation promotes a healthier and more stable gut ecosystem in weaned piglets through coordinated modulation of microbial composition, functional potential, and metabolic outputs. This study provides novel insights into microbiota-metabolite interactions underlying phytogenic interventions and supports the use of Lonicera japonica as a natural feed additive to enhance intestinal health and resilience during weaning.},
}

@article {pmid42344904,
year = {2026},
author = {Guo, R and Chen, Q and Kong, L and Huang, A and Li, Y and Li, C},
title = {Anti-NMDAR and anti-MOG antibody double-positive encephalitis temporally associated with cytomegalovirus detection in cerebrospinal fluid: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1805851},
pmid = {42344904},
issn = {1664-3224},
mesh = {Humans ; Male ; Middle Aged ; *Cytomegalovirus/immunology/genetics ; *Cytomegalovirus Infections/immunology/diagnosis/drug therapy/cerebrospinal fluid/complications ; *Autoantibodies/cerebrospinal fluid/blood ; *Receptors, N-Methyl-D-Aspartate/immunology ; Antiviral Agents/therapeutic use ; DNA, Viral/cerebrospinal fluid ; Myelin-Oligodendrocyte Glycoprotein ; },
abstract = {The co-occurrence of MOG and NMDAR antibodies has been reported in a limited number of cases and is termed the overlapping syndrome (MNOS). Viral coinfections have been identified in a subset of patients with MNOS. Herein, we report the first case of MNOS with concomitant cytomegalovirus (CMV) infection detected in cerebrospinal fluid, a finding that helps to further explore the relationship between viral infection and MNOS. A previously healthy 49-year-old man developed fever and behavioral abnormalities following prodromal symptoms. Metagenomic next-generation sequencing (NGS) of the CSF identified CMV DNA with high confidence (specific reads: 362; relative abundance: 85.97%). Serology was positive for CMV IgG but negative for IgM; serum CMV-DNA detected by real-time PCR was negative. Positivity for anti-NMDAR antibodies and anti-MOG antibodies in the CSF, whereas only anti-MOG antibodies were detected in the serum. The patient's condition gradually improved after treatment with antiviral agents, corticosteroids, and intravenous immunoglobulin. The main limitations of this report include the lack of detection of CMV-DNA in CSF by real-time PCR, as well as the absence of dynamic assessment of serum/CSF CMV IgG/IgM, anti-NMDAR, and MOG antibody titers. Clinical vigilance for coexisting autoimmune encephalitis should be heightened following viral infections.},
}

Humans
Male
Middle Aged
*Cytomegalovirus/immunology/genetics
*Cytomegalovirus Infections/immunology/diagnosis/drug therapy/cerebrospinal fluid/complications
*Autoantibodies/cerebrospinal fluid/blood
*Receptors, N-Methyl-D-Aspartate/immunology
Antiviral Agents/therapeutic use
DNA, Viral/cerebrospinal fluid
Myelin-Oligodendrocyte Glycoprotein

@article {pmid42345796,
year = {2026},
author = {Mancini, P and Brandtner, D and Cordeschi, G and Iaconelli, M and Mastrantonio, V and La Rosa, G and Porretta, D},
title = {Exploratory Metaviromic Analysis of the Sea-Rock Pool Mosquito Aedes mariae and the Water of Its Breeding Habitat.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/biology15120940},
pmid = {42345796},
issn = {2079-7737},
abstract = {The mosquito-associated virome may modulate host biology and influence vector competence, highlighting the importance of understanding its composition. Here, a metagenomic analysis was conducted to characterize the virome of the sea-rock pool mosquito Aedes mariae across sexes and developmental stages, together with water from its sea-rock pool breeding site in San Felice Circeo (Italy). A total of 51 viral taxa were identified, including viruses associated with bacteria and archaea (39%), plants, algae, fungi, and protists (35%), vertebrates (8%), and invertebrates (18%), including insect-specific viruses such as Mesoniviridae, Baculoviridae, Nudiviridae, Iridoviridae and Totiviridae. Twenty-five percent of the taxa were shared across samples, suggesting acquisition from breeding-site water and persistence across stages during development. Interestingly, the need for host genome filtering highlights the potential sequence similarity between viral and mosquito genomes, which may reflect the presence of endogenous viral elements or historical virus-host interactions. These findings represent the first characterization of the virome of Aedes mariae and highlight the role of aquatic breeding sites in shaping mosquito virome. Finally, we argue the importance of adequate sequencing depth and host genome filtering to capture the diversity of the mosquito virome.},
}

@article {pmid42345825,
year = {2026},
author = {Zhakypbek, Y and Toktar, M and Kossalbayev, BD and Yang, Q and Shi, Q and Tursbekov, S and Belkozhayev, AM and Abseyt, AS and Kezembayeva, G and Kamarkhan, T},
title = {Soil Bacterial Community Structure and Functional Potential in the Caspian Drylands of Western Kazakhstan.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/biology15120969},
pmid = {42345825},
issn = {2079-7737},
support = {BR24993218//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3-V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies.},
}

@article {pmid42346014,
year = {2026},
author = {Domingues, R and Pires, JCM},
title = {Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.},
journal = {Biotech (Basel (Switzerland))},
volume = {15},
number = {2},
pages = {},
pmid = {42346014},
issn = {2673-6284},
support = {UID/00511/2025 and UID/PRR/00511/2025//Fundação para a Ciência e Tecnologia/ ; LA/P/0045/2020//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Understanding biological communities is essential for elucidating ecosystem structure and function. Metabarcoding based on ribosomal RNA (rRNA) genes, particularly 16S and 23S, is widely used to characterise bacterial and microalgal communities. However, analysing high-throughput sequencing data generated by platforms such as the Illumina MiSeq remains challenging due to fragmented bioinformatics tools, complex parameterisation, and limited accessibility for non-specialist users. In this study, a comprehensive and user-friendly bioinformatics pipeline is proposed for the analysis of 16S and 23S paired-end metabarcoding data. The workflow integrates all critical processing steps, including read merging, primer and adapter trimming, quality filtering, dereplication, chimaera removal, and clustering into Operational Taxonomic Units (OTUs). Taxonomic assignment is performed using curated reference databases, namely EZBioCloud for bacterial communities and µgreen for microalgae. The pipeline was developed in Python 3.11 and incorporates validated tools such as VSEARCH and Cutadapt, ensuring robustness and computational efficiency. Additionally, modules for alpha and beta diversity analysis are included to support comprehensive ecological interpretation. The main novelty of this work lies in providing a unified, GUI-based framework that enables the standardised processing of dual-marker (16S/23S) metabarcoding data within a single environment. In its current implementation, SOMBA supports the analysis of each marker through separate but harmonised workflows, ensuring consistency in parameterisation, processing steps, and output structure. This approach provides an accessible and standardised solution that bridges the gap between raw sequencing data and reliable biological insights, supporting applications in environmental microbiology and biotechnology.},
}

@article {pmid42346116,
year = {2026},
author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M},
title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.},
journal = {Cells},
volume = {15},
number = {12},
pages = {},
pmid = {42346116},
issn = {2073-4409},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.},
}

Humans
Multiomics
*Neurodegenerative Diseases/immunology/metabolism
Animals
*Brain/immunology/metabolism
*Metabolic Diseases/immunology/metabolism
Gastrointestinal Microbiome
Metabolomics

@article {pmid42346385,
year = {2026},
author = {Li, J and Xu, X and Wang, H and Gao, R and Li, B and You, X},
title = {Relationship Between Calcium and Gut Microbial Composition and Metabolic Pathways in Children with Autism.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060405},
pmid = {42346385},
issn = {2218-1989},
support = {531100006787540685//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; },
abstract = {Background/Objectives: Trace elements may influence autism spectrum disorder (ASD) severity through interactions with the gut microbiota and microbial metabolic functions, but calcium-related evidence remains limited. This cross-sectional study examined associations among hair calcium, gut microbial taxa, metabolic pathways, and behavioral phenotypes in children with ASD. Methods: We analyzed 183 children with ASD who had behavioral assessments, hair calcium measurements, and fecal shotgun metagenomic sequencing data. Participants in the lowest and highest calcium quartiles were first compared to characterize group-level microbiome differences. Full-sample analyses then tested associations among continuous hair calcium, microbial taxa, metabolic pathways, and behavioral measures after covariate adjustment. Benjamini-Hochberg false discovery rate correction was applied for multiple testing. Results: Hair calcium was positively associated with CARS, ATEC-Total, ATEC-1, and ATEC-3 scores, with the strongest associations involving ATEC-1 and ATEC-3. Alpha and beta diversity did not differ significantly between calcium quartile groups, but group-based microbiome analyses identified 63 differential species and 22 differential MetaCyc pathways. Full-sample integrated analyses connected calcium-associated microbial taxa, metabolic pathways, and ASD behavioral measures. Conclusions: Hair calcium was associated with ASD behavioral severity, selected gut microbial species, and microbial metabolic pathways. These findings support an association framework connecting longer-term calcium-related mineral profiles, gut microbial functional potential, and behavioral phenotypes, providing a basis for future longitudinal and multi-omics studies.},
}

@article {pmid42346775,
year = {2026},
author = {He, Z and Nie, Y and Li, C and Sun, G and Zheng, W and Liu, H and Geng, M and Tian, J and Zhang, Y},
title = {GV-971 Ameliorates Chronic Restraint Stress-Induced Depression-like Phenotypes Accompanied by Reshaping of the Microbiota-Gut-Brain Axis.},
journal = {Marine drugs},
volume = {24},
number = {6},
pages = {},
pmid = {42346775},
issn = {1660-3397},
support = {2024CXPT029, 2025CXPT011//Key R&D Program of Shandong Province, China/ ; ZR2024QH615//Shandong Provincial Natural Science Foundation/ ; SYS202205//Shandong Laboratory Program/ ; },
mesh = {Animals ; *Depression/drug therapy/etiology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Brain-Gut Axis/drug effects ; *Oligosaccharides/pharmacology ; Restraint, Physical ; Disease Models, Animal ; *Antidepressive Agents/pharmacology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; Phenotype ; Hippocampus/drug effects/metabolism ; Intestinal Barrier Function ; },
abstract = {Depression is increasingly linked to microbiota-gut-brain axis dysfunction, yet current monoaminergic antidepressants show limited efficacy. This study investigated the therapeutic potential and underlying mechanisms of GV-971, a marine-derived oligosaccharide, in a chronic restraint stress (CRS) mouse model. We first established that 8 h of daily restraint for 4-8 weeks induces a stable depression-like phenotype characterized by behavioral despair and significant reduction in peripheral monoamine neurotransmitters (5-HT and norepinephrine). GV-971 treatment robustly attenuated CRS-induced depression- and anxiety-like behaviors, restored hippocampal serotonin levels, reduced elevated plasma corticosterone concentrations, and ameliorated CRS-induced adrenal cortical hyperplasia. Mechanistically, GV-971 significantly suppressed neuroinflammation by inhibiting microglial hyperactivation in the prefrontal cortex and hippocampus. Concurrently, it repaired intestinal barrier dysfunction, evidenced by reduced permeability, restored mucosal integrity, and recovered goblet cell numbers. Crucially, integrated shot-gun metagenomics and plasma metabolomics revealed that GV-971 not only reshaped microbial taxonomy but also functionally recalibrated the gut ecosystem. It enriched beneficial taxa (e.g., Bifidobacterium pseudolongum, Bacteroides uniformis) and specific metabolic pathways, leading to increased short-chain fatty acids (valeric and caproic acids) and a significant reduction in plasma levels of tryptophan-kynurenine pathway metabolites, specifically the neurotoxic compounds kynurenine and quinolinic acid. Fecal microbiota transplantation (FMT) from GV-971-treated donors partially recapitulated the antidepressant and gut-protective effects in CRS recipients, confirming a causal role for the remodeled microbiota. Collectively, GV-971 exerts antidepressant effects by coordinately remodeling the gut microbiota, normalizing tryptophan and SCFA metabolism, restoring gut barrier integrity, and dampening central neuroinflammation, supporting its potential as a novel gut-brain axis-targeted therapy for depression.},
}

Animals
*Depression/drug therapy/etiology
*Gastrointestinal Microbiome/drug effects
Male
Mice
*Stress, Psychological/drug therapy
*Brain-Gut Axis/drug effects
*Oligosaccharides/pharmacology
Restraint, Physical
Disease Models, Animal
*Antidepressive Agents/pharmacology
Mice, Inbred C57BL
Brain/drug effects/metabolism
Phenotype
Hippocampus/drug effects/metabolism
Intestinal Barrier Function

@article {pmid42347203,
year = {2026},
author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ},
title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060591},
pmid = {42347203},
issn = {2076-0817},
mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration & dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration & dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration & dosage ; },
abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.},
}

Humans
Child
Pilot Projects
Female
Probiotics/administration & dosage
Male
*Microbiota
*Growth Disorders/microbiology/complications
Mouthwashes/administration & dosage
*Mouth/microbiology
Saliva/microbiology/chemistry
Oral Health
Bacteria/classification/genetics
Oils, Volatile/administration & dosage

@article {pmid42347234,
year = {2026},
author = {Wojnarowski, K and Cholewińska, P and Zhao, D and Hasegawa, Y and Denk, D and Palić, D},
title = {Rapid Culture-Independent Detection of Fish Pathogens Using Oxford Nanopore Technologies: Case-Based Insights Across Multiple Species and Tissues.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060622},
pmid = {42347234},
issn = {2076-0817},
mesh = {Animals ; *Fish Diseases/microbiology/diagnosis ; *Bacteria/genetics/classification/isolation & purification ; *Nanopore Sequencing/methods ; Fishes/microbiology ; Metagenomics/methods ; *Bacterial Infections/veterinary/diagnosis/microbiology ; },
abstract = {Rapid and accurate diagnosis of infectious diseases in aquaculture is essential for preventing major economic and ecological losses. Traditional culture-based methods focus on isolation of individual pathogens, and often are burdened with extended processing times, particularly during investigations of polymicrobial infections. Application of Oxford Nanopore Technologies (ONT) sequencing offers a rapid, culture-independent workflow for the identification of bacterial and fungal pathogens directly from fish tissues. Swab and organ samples from four cases (1: Salmo spp.; 2: Cyprinus carpio; 3: Salvelinus fontinalis; 4: Heniochus acuminatus) were analyzed using ONT long-read sequencing for metagenomic screening and bioinformatic classification. The results revealed case-, species-, and tissue-specific microbial profiles, with external tissues showing higher microbial diversity and internal organs enriched in pathogenic taxa. Dominant pathogens included Streptococcus iniae, Aeromonas hydrophila, Pseudomonas spp., and Saprolegnia parasitica, alongside opportunistic zoonotic bacteria such as Escherichia coli and Acinetobacter baumannii. We demonstrate the potential for diagnostic application of ONT sequencing in investigations and detection of multi-pathogen infections, including assessments of microbial community structure changes during disease outbreaks in aquatic species. The presented workflow enables rapid, cost-effective, and comprehensive pathogen profiling, supporting early disease surveillance and improved management in aquatic veterinary practice.},
}

Animals
*Fish Diseases/microbiology/diagnosis
*Bacteria/genetics/classification/isolation & purification
*Nanopore Sequencing/methods
Fishes/microbiology
Metagenomics/methods
*Bacterial Infections/veterinary/diagnosis/microbiology

@article {pmid42347240,
year = {2026},
author = {Chen, J and Wang, H and Li, Y and Xiao, Y and Yan, Y and Zhang, Y and Lu, X},
title = {Scenario-Driven Rapid Testing for Top Pathogens in Pediatric Respiratory Infections: Clinical and Economic Value from Emergency Triage to Precision Anti-Infective Management in the PICU.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060628},
pmid = {42347240},
issn = {2076-0817},
support = {WJ2025Z010//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; WX23A90//Wuhan Health Commission/ ; 32270528//National Natural Science Foundation of China/ ; CX20240883//Hunan Provincial Postgraduate Research and Innovation Project/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/drug therapy/microbiology/virology ; *Triage ; Intensive Care Units, Pediatric ; Rapid Diagnostic Tests ; Child ; Anti-Bacterial Agents/therapeutic use ; *Anti-Infective Agents/therapeutic use ; },
abstract = {Pediatric respiratory infections remain among the leading causes of emergency department visits, hospitalization and pediatric intensive care unit (PICU) admission. Although most acute respiratory infections in children are viral, clinical manifestations overlap substantially among viral, bacterial and atypical pathogens, creating diagnostic uncertainty and promoting empirical antimicrobial use. Rapid antigen tests, nucleic acid amplification tests, multiplex respiratory panels and metagenomic sequencing have expanded the ability to detect pathogens within clinically actionable timeframes. However, evidence from pediatric emergency trials indicates that rapid pathogen detection alone does not necessarily reduce antibiotic prescribing or healthcare costs. These findings suggest that the value of rapid diagnostics depends less on analytical breadth than on whether testing is applied to the right child, in the right clinical scenario and within a predefined decision pathway. This narrative review reorganizes the evidence around a scenario-driven top-pathogen framework. Top pathogens are defined as organisms that, in a specific age group, syndrome, season or care setting, have high prevalence, severe disease potential, transmissibility, treatment implications, antimicrobial resistance relevance or infection-control value. We discuss how top-pathogen testing should differ across emergency triage, inpatient ward management, severe pneumonia, PICU care, hospital-acquired pneumonia, ventilator-associated pneumonia and outbreak settings. We further examine the economic mechanisms through which rapid testing may generate value, including reduced unnecessary antibiotics, timely antiviral therapy, optimized isolation, shorter length of stay, reduced repeated testing and prevention of healthcare-associated transmission. Finally, we propose implementation principles centered on diagnostic stewardship, antimicrobial stewardship, local epidemiology and real-world cost-effectiveness evaluation. A scenario-driven top-pathogen strategy may provide a practical bridge between broad syndromic testing and precision infectious disease management in children.},
}

Humans
*Respiratory Tract Infections/diagnosis/drug therapy/microbiology/virology
*Triage
Intensive Care Units, Pediatric
Rapid Diagnostic Tests
Child
Anti-Bacterial Agents/therapeutic use
*Anti-Infective Agents/therapeutic use

@article {pmid42347253,
year = {2026},
author = {Yean, S and Prasetyo, DB and Chao, S and Vuth, L and Prot, M and Baidaliuk, A and Bonnet, S and Simon-Loriere, E and Boyer, S},
title = {Combining PCR and Metagenomic Approaches to Reveal Tick-Borne Pathogens in Ticks Collected from Livestock and Companion Animals in Cambodia.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060641},
pmid = {42347253},
issn = {2076-0817},
mesh = {Animals ; Cambodia/epidemiology ; *Tick-Borne Diseases/veterinary/epidemiology/microbiology ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Livestock/parasitology ; Cross-Sectional Studies ; Cattle ; *Ticks/microbiology/virology/parasitology ; Dogs ; Tick Infestations/veterinary ; Bacteria/genetics/isolation & purification/classification ; },
abstract = {In Cambodia, livestock production plays an important role in the national economy and food security, yet tick-borne diseases remain an underrecognized constraint on animal health and productivity. Domestic animals may also serve as reservoirs of zoonotic pathogens in this predominantly rural setting. To address the lack of baseline molecular data on tick-borne pathogens in Cambodia, we conducted a cross-sectional study of ticks collected from November 2022 to April 2023 across 24 provinces. Ticks were collected from various hosts and environments, including cats, cattle, dogs, goats, pangolins, pythons, wild pigs, and bat cave floors, representing urban, rural, farm, wildlife rescue center, and forest fringe habitats. A total of 1526 ticks belonging to nine species were pooled into 352 samples and screened using conventional PCR (cPCR) targeting Anaplasma, Ehrlichia, Babesia, and Coxiella. Additionally, a subset of Rhipicephalus microplus ticks was analyzed using metatranscriptomic next-generation sequencing (NGS). Rhipicephalus microplus ticks collected from cattle tested positive for Anaplasma marginale (1.1% of pools) and Ehrlichia minasensis (0.9% of pools), whereas Rhipicephalus linnaei ticks collected from dogs were positive for Anaplasma platys (0.3% of pools) and Babesia canis (2.0% of pools). A high prevalence of Coxiella-like endosymbionts (15.6% of pools) was found in R. microplus from both cattle and goats. Metatranscriptomic analysis also identified six tick-associated viruses in R. microplus from cattle; with Guangdong tick manly virus being the most dominant (32.5% of samples); followed by Zhangzhou Totiv tick virus 1 (15.0%), Jingmen tick virus (5.0%), and Mogiana tick virus; Rhipicephalus-associated rhabdo-like virus; and Rhipicephalus-associated flavi-like virus; each at 2.5%. These findings provide the first molecular evidence of numerous bacterial, protozoal, and viral pathogens circulating in R. microplus and R. linnaei in Cambodia. The study highlights the need for integrated One Health surveillance to better understand, prevent, and control tick-borne diseases in the region.},
}

Animals
Cambodia/epidemiology
*Tick-Borne Diseases/veterinary/epidemiology/microbiology
*Metagenomics/methods
*Polymerase Chain Reaction/methods
*Livestock/parasitology
Cross-Sectional Studies
Cattle
*Ticks/microbiology/virology/parasitology
Dogs
Tick Infestations/veterinary
Bacteria/genetics/isolation & purification/classification

@article {pmid42347401,
year = {2026},
author = {Zheng, L and He, Y and Yan, Y and Li, Q and Zhang, L and Xing, Z and Lu, X},
title = {Characteristics, Ecological Risks, and the Impacts on Soil Carbon Cycling of PAH Pollution in the Soil of a Retired Coking Plant in Zaozhuang, Northern China.},
journal = {Toxics},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/toxics14060503},
pmid = {42347401},
issn = {2305-6304},
abstract = {During the industrial restructuring in China, numerous outdated coking enterprises were phased out. Despite the cessation of production for several years, the soil in the production area of the retired coking plant remains heavily contaminated with polycyclic aromatic hydrocarbons (PAHs), which continue to adversely affect soil health. However, research on the pollution characteristics of soil PAHs under prolonged PAH exposure and the associated changes in functional genes related to soil carbon cycling is still inadequate. This study aims to identify the pollution characteristics and ecological risks of PAHs in the coking plant and to investigate the effects of long-term PAH contamination from abandoned coking plants on the functional genes involved in soil carbon cycling. It was found that PAHs in the soil were predominantly composed of high-molecular-weight PAHs (HMW-PAHs), which constituted 65.7% to 83.4% of the total PAH content. The total concentration of PAHs in the surface soil ranged from 3.79 to 554 mg·kg[-1], with an average concentration of 147.6 mg·kg[-1]. Source analysis based on isomer ratios indicated that PAHs primarily originated from the combustion of coal and biomass. Utilizing the toxicity equivalent factor (TEF) method, we found that the PAH levels in the CA group exceeded the Serious Risk Concentration, indicating that PAH pollution poses a potential threat to the ecological environment. Metagenomic analysis revealed that the gene abundance of alpha-amylase in the CA group was significantly higher than that in the OLA group (p < 0.05), suggesting that prolonged exposure to PAHs has enhanced the starch hydrolysis capabilities of soil microorganisms. The findings of this study refine methods for assessing the risks associated with soil PAH contamination and provide a theoretical foundation for the risk management and reuse of retired coking plant sites.},
}

@article {pmid42347555,
year = {2026},
author = {Jacob, SM and Akinbo, SY and Ajakaye, OG and Ekpo, UF and Omoruyi, Z and Agbana, T and Makau-Barasa, L and Aderogba, MO and Diehl, JC and Bell, D and Bayegun, AA and Okungbowa, MA and A-Enegela, J and Akinbo, FO},
title = {Molecular Identification of Schistosoma Species Associated with Atypical Urinary Eggs in Abuja (Nigeria): Evidence of Potential Zoonotic Transmission.},
journal = {Tropical medicine and infectious disease},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/tropicalmed11060170},
pmid = {42347555},
issn = {2414-6366},
abstract = {Schistosomiasis remains a major public health concern in Nigeria. We molecularly characterized Schistosoma eggs obtained from human urine to identify species and assess the presence of hybrid schistosomes in Abuja, Nigeria. Urine samples were collected from 1887 participants aged five years and above. Samples were examined for Schistosoma eggs using light microscopy. A total of 507 (26.9%) were positive for any form of Schistosoma while 91 (4.8%) had atypical Schistosoma eggs. DNA extracted from pooled ova was analyzed using metagenomic sequencing, read mapping, phylogenetic analysis, and BLASTn confirmation. Molecular analyses identified genetic signatures associated with both S. haematobium and S. bovis within pooled human urine samples, indicating the co-circulation of multiple schistosome species in the study area. Phylogenetic analyses based on trans-ITS and mitochondrial COX1 markers supported the presence of distinct nuclear and mitochondrial schistosome lineages. However, because sequencing was performed on pooled egg samples, the findings cannot distinguish between true recombinants and mixed infections involving co-circulating parental species. These findings highlight the potential complexity of schistosome transmission dynamics in endemic communities and underscore the need for enhanced molecular surveillance, especially single-parasite genomic approaches, and integrated One Health investigations to better understand schistosome transmission and its implications for control and elimination efforts in Nigeria.},
}

@article {pmid42347906,
year = {2026},
author = {Liu, Y and Lin, H and Zhu, M and Chen, X and Yu, Z and Peng, D and Dong, G and Ni, Y and Fu, J},
title = {Gut microbiota dysbiosis and short-chain fatty acid alterations in pediatric new-onset type 1 diabetes with ketoacidosis.},
journal = {Journal of endocrinological investigation},
volume = {},
number = {},
pages = {},
pmid = {42347906},
issn = {1720-8386},
support = {2023C03047//Key Research and Development Program of Zhejiang Province/ ; 2021YFC2701900//Key Technologies Research and Development Program/ ; 82370863//National Natural Science Foundation of China/ ; 82502105//National Natural Science Foundation of China/ ; LKLY25H180005//Natural Science Foundation of Zhejiang Province/ ; LQN25H040005//Natural Science Foundation of Zhejiang Province/ ; },
abstract = {PURPOSE: Diabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication in children with type 1 diabetes (T1D) and remains associated with considerable morbidity and mortality. Although gut dysbiosis has been reported in newly diagnosed T1D, the gut microbiota and microbial metabolites during DKA onset remain poorly characterized.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 96 newly diagnosed T1D children, including 32 presenting with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative and correlation analyses were conducted to explore differences in gut microbial composition, SCFA levels, and their association with clinical indicators of DKA severity.

RESULTS: Children with DKA exhibited distinct gut microbial compositions, with marked β-diversity separation from non-DKA individuals. The DKA group was characterized by an enrichment of potential pathogens and a significant depletion of SCFA-producing genera, including Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus. Correspondingly, fecal SCFA levels were significantly reduced in the DKA group. Moreover, SCFAs and their producing bacteria were strongly correlated with clinical indices of DKA severity. Mediation analysis suggested that reductions in SCFAs, particularly propionic acid and butyric acid, were associated with metabolic alterations linking SCFA-producing bacteria to DKA.

CONCLUSION: This study provides a comprehensive characterization of gut microbiota and SCFA alterations in T1D children at DKA onset. The depletion of SCFA-producing bacteria and their metabolites reflects metabolic disturbances associated with DKA, and highlights SCFAs and their producers as candidate metabolic features warranting further validation as biomarkers and therapeutic targets.},
}

@article {pmid42347915,
year = {2026},
author = {Huang, CH and Lu, IC and Lin, CW and Hsieh, MT and Chiang, IH and Lai, PH and Liu, IT and Chen, JS},
title = {Gut microbiota profiles across intrinsic capacity strata in community-dwelling older adults using full-length 16S rRNA sequencing.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42347915},
issn = {2509-2723},
support = {NSTC 112‑2314‑B‑650‑001‑MY3//National Science and Technology Council/ ; EDAHP111045//E-Da Hospital/ ; EDAHP113004//E-Da Hospital/ ; EDAHS113021//E-Da Hospital/ ; },
abstract = {Intrinsic capacity (IC), introduced by the World Health Organization, provides a multidimensional framework for evaluating functional aging across locomotion, cognition, sensory, psychological, and vitality domains. However, gut microbial features associated with IC among community-dwelling older adults remain incompletely understood. In this exploratory cross-sectional study, we enrolled 52 community-dwelling older adults and assessed gut microbiota using full-length 16S rRNA sequencing. Participants were stratified into IC quartiles, and additional analyses examined composite IC and domain-specific IC scores as continuous measures. Alpha diversity indices were not significantly associated with composite IC after false discovery rate correction, although vitality showed nominal positive associations with observed features and Chao1 richness (both rho = 0.316, P = 0.024, q = 0.288). PERMANOVA did not show statistically robust differences in beta diversity across IC quartile groups using Bray-Curtis distance (R[2] = 0.061, P = 0.060, q = 0.383), weighted UniFrac distance (R[2] = 0.083, P = 0.140, q = 0.436), or unweighted UniFrac distance (R[2] = 0.063, P = 0.211, q = 0.443). Selected bacterial taxa, including Ruminococcaceae, Lachnospiraceae, Alistipes, and Faecalibacterium, showed nominal associations with composite or domain-specific IC measures, but none remained significant after FDR correction or covariate-adjusted regression. In PICRUSt2-predicted functional analyses, several COG features related to transport systems, multidrug efflux, and site-specific recombination were positively associated with the vitality domain after false discovery rate correction. Because functional profiles were inferred from 16S rRNA sequencing rather than directly measured by shotgun metagenomics, metabolomics, or inflammatory biomarkers, these findings should be interpreted as exploratory and hypothesis-generating. This study identifies candidate microbiota and predicted functional features for future longitudinal and mechanistic studies of multidimensional functional aging.},
}

@article {pmid42348069,
year = {2026},
author = {Ernst, S and Dirschka, T},
title = {The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42348069},
issn = {2193-8210},
abstract = {The human facial skin microbiome is a complex and dynamic ecosystem that plays a central role in maintaining skin health, immune regulation, and preventing dermatological skin conditions. Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) are the most prominent bacterial species, with shifts in their relative abundance correlating with skin site, age, skin site, and health status. Exploring the facial microbiome offers exciting opportunities, though it requires careful methodological consideration. Sampling techniques vary in invasiveness and depth, which can influence the accuracy and reproducibility of microbiome profiles. While traditional cultivation methods provide valuable insights, they often miss nonculturable microbes, limiting the view of microbial diversity. Molecular approaches such as amplicon sequencing and metagenomics enable a more comprehensive understanding of microbial communities, even though they currently cannot distinguish between viable and nonviable microbes. Addressing these challenges will help unlock the full potential of facial microbiome research. A balanced facial skin microbiome is associated with healthy skin, whereas a dysbiosis of C. acnes and S. epidermidis is commonly observed in acne-prone skin and more pronounced clinically manifest acne. A comprehensive understanding of the diversity and distribution of C. acnes phylotypes, as well as distinct lineages of S. epidermidis associated with skin disorders, is crucial for developing targeted, microbiome-based cosmetic and medical treatments. Emerging strategies aim to restore microbial balance by leveraging the skin's native microbiota, including probiotic approaches. These strategies represent a promising yet still emerging approach, as current clinical evidence remains limited and further well-controlled studies are required, although they may offer benefits by enhancing microbial diversity and supporting skin barrier function.},
}

@article {pmid42348335,
year = {2026},
author = {Biswa, BB and Mori, H and Toyoda, A and Fujiwara, K and Kurokawa, K and Koide, T},
title = {Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {33},
number = {3},
pages = {},
doi = {10.1093/dnares/dsag006},
pmid = {42348335},
issn = {1756-1663},
support = {JPMJSP2104//JST/ ; 19KK0177//JSPS/ ; 24K01951//JSPS/ ; //Research Organization of Information and Systems/ ; },
mesh = {Animals ; Male ; Female ; *Limosilactobacillus reuteri/isolation & purification/genetics ; Mice ; Oxytocin/blood ; *Behavior, Animal ; *Gastrointestinal Microbiome ; Feces/microbiology ; Selective Breeding ; Pyruvic Acid/blood ; },
abstract = {Domestication alters animal behaviour, particularly tameness. We previously established 2 tamed mouse groups by selective breeding for active tameness-defined as the motivation to approach a human hand-from genetically heterogeneous wild-derived mouse stock, together with 2 nonselected control groups. Genetic analyses identified loci associated with active tameness, but their low heritability suggested contributions from nongenetic factors. We therefore hypothesized that the gut microbiota, which has been shown to influence brain function, contributes to behavioural changes associated with active tameness. To test this hypothesis, we conducted shotgun metagenomic analyses of faecal samples from 10 males and 10 females (80 individuals total) from the 2 tamed and 2 nonselected groups. Tamed mice exhibited markedly higher levels of active tameness, accompanied by elevated blood concentrations of oxytocin and pyruvate. While overall taxonomic and functional diversity of the gut microbiota was largely unchanged, the abundance of Limosilactobacillus reuteri was significantly increased in the tamed mice. Administration of a pyruvate-secreting L. reuteri strain to nonselected mice elevated blood oxytocin levels and enhanced active tameness, although plasma pyruvate levels were not increased. These findings suggest that L. reuteri is associated with behavioural modulation, potentially via oxytocin-related pathways, and provide mechanistic insight into microbial contributions to animal domestication.},
}

Animals
Male
Female
*Limosilactobacillus reuteri/isolation & purification/genetics
Mice
Oxytocin/blood
*Behavior, Animal
*Gastrointestinal Microbiome
Feces/microbiology
Selective Breeding
Pyruvic Acid/blood

@article {pmid42348560,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0352336},
doi = {10.1371/journal.pone.0352336},
pmid = {42348560},
issn = {1932-6203},
mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; },
abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.},
}

Animals
*Dairying/methods
*Microbiota/genetics
Cattle
Milk/microbiology
Farms
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial/genetics
Metagenome
Metagenomics
Organic Agriculture

@article {pmid42349033,
year = {2026},
author = {Cárdenas-Conejo, Y},
title = {GenomoBase: A comprehensive resource for the family Genomoviridae.},
journal = {Virology},
volume = {623},
number = {},
pages = {111018},
doi = {10.1016/j.virol.2026.111018},
pmid = {42349033},
issn = {1096-0341},
abstract = {The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run reconstructed two candidate complete circular genomovirus genomes from metagenomic reads, both below the 78% species demarcation threshold for genomoviruses. Overall, GenomoBase supports comparative analyses and taxonomically informed exploration of public metagenomes.},
}

@article {pmid42349155,
year = {2026},
author = {Li, YY and Lin, L and Wen, L and Li, XY},
title = {Rapid adaptation and enrichment of salt-tolerant anammox via dosing of chemical enhancers in packed-bed biofilm reactor.},
journal = {Water research},
volume = {304},
number = {},
pages = {126343},
doi = {10.1016/j.watres.2026.126343},
pmid = {42349155},
issn = {1879-2448},
abstract = {The application of anammox-based processes for saline wastewater treatment is constrained by the scarcity of salt-tolerant seed sludge and the lengthy adaptation periods. To overcome this challenge, exogenous chemical enhancers, hydrazine (N2H4, 5 mg/L) and glycine betaine (GB, 30 mg/L), were introduced and evaluated for their roles in facilitating salt-adapted anammox biofilms enrichment from freshwater seed in packed-bed biofilm reactors. Hydrazine addition for 15 days increased the nitrogen removal rate from approximately 50 to 441.1 mg N/(L·d) within 70 days, which was substantially higher than that achieved through natural acclimation (192.2 mg N/(L·d)). When GB was subsequently supplemented for 30 days to the naturally acclimated reactor, its nitrogen removal rate rapidly increased to 1000 mg N/(L·d) within 30 days and further to 3000 mg N/(L·d) within 60 days, catching up the reactor receiving N2H4 from the outset. According to community analysis, performance recovery coincided with immediate shift from Ca. Brocadia to Ca. Kuenenia, with its relative abundance surged ∼15-fold within 20 days, highlighting the remarkable stimulatory effect of enhancers on Ca. Kuenenia's proliferation. Inferred from KEGG pathway studies, N2H4 primarily enhanced oxidative phosphorylation and ATP synthesis, providing energetic support for early recovery of the proton motive force and osmotic balance. In contrast, GB stabilized cellular osmotic conditions and membrane structures, enabling reallocation of metabolic resources toward antioxidant defense, cellular repair, and folate biosynthesis under saline stress. This alleviated the energetic burden associated with ion transport and lipid remodeling, thereby promoting sustained recovery of the anammox community.},
}

@article {pmid42349523,
year = {2026},
author = {Muqaddas, K and Mahnoor, and Hayat, O and Islam, A and Khan, R and Naz, S},
title = {Cutaneous Leishmaniasis Promotes Skin Microbial Dysbiosis and Exacerbation of Local Inflammatory Responses.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.micpath.2026.108655},
pmid = {42349523},
issn = {1096-1208},
abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.},
}

@article {pmid42349567,
year = {2026},
author = {Wang, J and Wen, J and Zhang, X and Zhang, X and Wu, P},
title = {Sulfide-mediated anammox performance under antibiotics stress: Linking antibiotic resistance genes, functional microbes and nitrogen-sulfur metabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135244},
doi = {10.1016/j.biortech.2026.135244},
pmid = {42349567},
issn = {1873-2976},
abstract = {Anaerobic ammonium oxidation (anammox), a sustainable and energy-efficient biological nitrogen removal process, is vulnerable to antibiotic stress during stable operation, while the mechanism of functional recovery mediated by sulfides remains unclear. This study systematically analyzed the response characteristics of the anammox process under sustained high-concentration oxytetracycline (OTC) and sulfamethoxazole (SMX) exposure, and further evaluated the potential of sulfide as an exogenous regulatory factor to mitigate antibiotic stress. Results indicate that sustained high concentration OTC and SMX exposure impaired the system's nitrogen removal performance, while the removal efficiencies of ammonium and nitrite successfully recovered to 85% and 83%, respectively, following sulfide addition. Metagenomic analysis suggested that the addition of sulfide was accompanied by an increased abundance of potential genes related to sulfur and nitrogen metabolism. Moreover, sulfide may alleviate antibiotic stress by facilitating metabolic interactions related to electron transfer and increasing the potential for SMX degradation. Furthermore, under OTC and SMX stress, a 20% increase in the abundance of Brocadia sapporoensis harboring ARGs was closely associated with the addition of sulfide. This study elucidates the biological mechanisms by which sulfides mitigate antibiotic stress, providing a theoretical basis for recovery strategies of anammox under an intensified stress model.},
}

@article {pmid42349748,
year = {2026},
author = {Ortega-Yago, A and Rubio, P and Ulldemolins, P and Baeza-Oliete, J and Bas, P and Bas, T},
title = {What's new in spinal instrumentation-related infections.},
journal = {Revista espanola de cirugia ortopedica y traumatologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.recot.2026.06.008},
pmid = {42349748},
issn = {1988-8856},
abstract = {Infections associated with spinal instrumentation represent one of the most complex complications in spine surgery and frequently involve biofilm-forming pathogens that compromise the effectiveness of antimicrobial therapies. Diagnosis-particularly in chronic cases-requires the use of advanced microbiological techniques, such as implant sonication, next-generation metagenomic sequencing, and prolonged culture incubation. Therapeutic strategies depend on the chronicity of the infection and the stability of the implant, ranging from surgical debridement with retention of osteosynthesis material to staged delayed re-instrumentation. Empirical antibiotic therapy should be initiated promptly and subsequently adjusted according to microbiological results. Prevention remains a fundamental pillar and includes strict perioperative optimization. Favorable outcomes rely on early detection, a multidisciplinary team approach, and individualized surgical and antimicrobial management based on accurate clinical and radiological assessment.},
}

@article {pmid42349820,
year = {2026},
author = {Zhou, Y and Zhong, WJ and An, XL and Huang, FY and Guo, XY and Gao, MK and Xu, MR and Huang, X and Li, H and Zhang, B and Springael, D and Su, JQ},
title = {FThe ISChip: A High-Throughput qPCR Array for Absolute Quantification of Insertion Sequences across the One Health Continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128649},
doi = {10.1016/j.envpol.2026.128649},
pmid = {42349820},
issn = {1873-6424},
abstract = {Insertion sequences (IS) are pivotal mobile genetic elements that shape bacterial genome plasticity and act as critical drivers of environmental genetic hazards by accelerating the dissemination of antimicrobial resistance. However, high-throughput, absolute quantification of IS elements across diverse environmental matrices remains a significant technical challenge, as conventional short-read metagenomics often lacks the sensitivity and resolution required for profiling low-abundance and highly repetitive targets. Here, we developed ISChip, a high-capacity qPCR array for the multiplexed absolute quantification of 183 prevalent IS elements, serving as a robust quantitative complement to metagenomics. The platform was rigorously validated using 119 primer sets, demonstrating high specificity, efficiency, and a superior absolute sensitivity (limit of quantification: 23-28 copies per reaction) compared to conventional qPCR. We applied ISChip to 69 anthropogenically impacted samples spanning 13 matrices, including air, wastewater, soil, and human/animal feces, representing a comprehensive One Health continuum. Our results revealed a distinct compartmentalization of IS communities and identified wastewater, sludge, sediments, and human feces as primary IS hotspots. Notably, we discovered a highly conserved "core IS assemblage" in human feces, suggesting a unique niche for IS-driven microbial evolution. By providing a scalable and absolute quantitative framework, this study uncovers the extreme spatial magnitude of these biological hazards, serving as a powerful tool for monitoring genetic pollution across the One Health framework.},
}

@article {pmid42350342,
year = {2026},
author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T},
title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {6},
pages = {499-510},
pmid = {42350342},
issn = {1007-8738},
abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.},
}

@article {pmid42350492,
year = {2026},
author = {Dini, H and Chenghang, S and Tong, X and Yixin, L and Tianchun, P and Shunfu, H and Yanqiang, Y and Yibo, H},
title = {Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01066-9},
pmid = {42350492},
issn = {2055-5008},
support = {32370552//National Natural Science Foundation of China/ ; 32325010//National Natural Science Foundation of China/ ; 2023YFF1304800//National Key Program of Research and Development of Ministry of Science and Technology/ ; },
abstract = {The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.},
}

@article {pmid42350494,
year = {2026},
author = {Beiko, RG and Tolman, J and Barawi, SS and Fares, M and Murthy, SSN and Knox, T and Mackie, CM and Grundke, I and Jeffery, NW and Stanley, RRE and Sieben, V and LaRoche, J},
title = {Automated eDNA and eRNA profiling for biodiversity monitoring in marine and freshwater ecosystems.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-58421-1},
pmid = {42350494},
issn = {2045-2322},
abstract = {Biodiversity monitoring is essential to measure the impacts of pollution, invasive species, and the longer-term effects of climate change. Automated samplers enable temporally flexible, remote collection of environmental DNA (eDNA), improving access to time-sensitive events. The Dartmouth Ocean Technologies (DOT) Preserving eDNA Sampler has proven effective in multi-month marine deployments, but further validation is needed across a broader range of habitats and water chemistries, and to establish its suitability for collection and assessment of environmental RNA (eRNA). In this study, we collected samples near the surface (1-1.5 m depth) of a brackish pond, a freshwater lake, and two marine harbours. We identified patterns of species turnover consistent with transitions among aquatic environments, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. Automated deployment in Halifax Harbour following a significant rainfall event detected nearly ten times as many probable fecal-associated bacteria by proportion at this site relative to Lunenburg Harbour. Preserved eRNA allowed the identification of taxa below the eDNA limit of detection. Our pilot study demonstrates the feasibility of using the DOT sampler for longer-term biomonitoring in a diverse range of aquatic habitats, yielding ecological insights that would not be attainable through manual sampling alone.},
}

@article {pmid42350644,
year = {2026},
author = {Suissa, D and Fidelle, M and Reich, E and Pham, TN and Thomas, S and Björk, JR and Liu, P and Zhao, L and Kitaoka, K and Piard, E and Lebhar, I and Tian, AL and Thelemaque, C and Alves Costa Silva, C and Deutsch, E and Loriot, Y and Segata, N and Piccinno, G and Hospers, GAP and Maleki Vareki, S and Silverman, MS and Lenehan, JG and Bataille, V and Boulate, D and Kuznetsova, T and Weersma, RK and Messaoudene, M and Durand, S and van der Aalst, CM and de Koning, HJ and Schuler-Thurner, B and de Vries, IJM and Rafie, E and Saliby, RM and Machaalani, M and Haferkamp, S and Schilling, B and Porcari, S and Ciccarese, C and Iacovelli, R and Cremolini, C and Choueiri, TK and Elkrief, A and Kroemer, G and Heinzerling, L and Chamoto, K and Ianiro, G and Routy, B and Derosa, L and Paragios, N and Zitvogel, L},
title = {Metabolic determinants of cancer immunotherapy outcomes identified by plasma profiling.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42350644},
issn = {1546-170X},
abstract = {Immune-checkpoint inhibitors benefit a subset of patients with advanced cancer, and the metabolic determinants of response remain unclear. Here, using targeted metabolomics and metagenomics, we profiled 4,336 plasma samples from 1,714 patients across five tumor types and 16 cohorts spanning Europe and North America, longitudinally sampled during five immune-checkpoint inhibitor-based treatment modalities, including fecal microbiota transplantation. A multimodal machine-learning framework integrating 154 metabolites with clinical variables identified five metabolites, age, body mass index and renal function as predictors of 12-month progression-free survival. The model achieved areas under the curve of 0.88 in training and 0.73 in validation cohorts of 105 and 30 patients, respectively and generalized across seven external cohorts. Histidine was a favorable prognostic feature of survival, whereas long-chain fatty acids and succinate were negatively associated with outcome. Histidine supplementation enhanced antitumor immunity in mice. Histidine-rich diets improved progression-free survival in patients lacking dysbiotic microbiome signatures associated with histidine catabolism.},
}

@article {pmid42337002,
year = {2026},
author = {Guéguen, LM and Mathieu, A and Pelletier, S and Woo, A and Misra, N and Moreau, M and Perin, O and Droit, A},
title = {META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59138-x},
pmid = {42337002},
issn = {2045-2322},
abstract = {Traditional case-control metagenomic studies are constrained by their dependence on taxonomic and functional databases. Because annotation occurs before differential analysis, they are limited to known elements and keep function and taxonomy separate. Although binning strategies have emerged to reconstruct genomes and mitigate this issue, they still require an assembly step, preventing the use of all available sequencing data. Here, we introduce META-DIFF, a pipeline based on differentially abundant k-mers independently of any prior annotation. From those k-mers, it reconstructs longer sequences and provides biological context, as well as the best set of unitigs to discriminate between conditions. Across both taxonomy-centric and functionally-centric benchmarks, it showed robust performance and displayed great reproducibility. It also behaved more conservatively than did other univariate methodologies, i.e. it maintained a high precision at the expense of recall, particularly in conditions of low fold-change and limited sequencing depth. The efficacy of META-DIFF was further validated through its application to a real-world colorectal cancer dataset, which produced both confirmatory and novel results compared with those of previous publications. The pipeline is able to exploit all reads and identify differentially abundant elements, including unknown DNA, prior to annotation. With the guidelines provided, META-DIFF provides users with great exploratory power to unravel microbiome changes.},
}

@article {pmid42337243,
year = {2026},
author = {Hoskinson, C and Dai, DLY and Petersen, C and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Turvey, SE},
title = {Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42337243},
issn = {2041-1723},
support = {[274CHI] and [EC1-144621]//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; [274CHI] and [EC1-144621]//AllerGen (AllerGen National Center of Excellence)/ ; [274CHI] and [EC1-144621]//Genome Canada (Génome Canada)/ ; },
mesh = {Humans ; *Malassezia/genetics/isolation & purification/physiology ; Infant ; Feces/microbiology ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Mycobiome ; Male ; Female ; Child, Preschool ; *Food Hypersensitivity/microbiology/immunology ; Child ; Metagenome ; Metagenomics ; *Hypersensitivity/microbiology ; },
abstract = {While early-life gut bacterial microbiota maturation has been well studied and linked to childhood disease, the development of the gut mycobiome remains poorly understood. Few studies have defined fungal succession in infancy, and even fewer have integrated fungal and bacterial maturation, allowing interkingdom analysis within the same individuals. In this study, we analyzed a subset of the CHILD Study Cohort (n = 1409 participants) and generated both ITS2 amplicon and shotgun metagenomic sequencing data from infant stool samples (n = 2256 samples). We hypothesized that the infant mycobiome follows predictable developmental trajectories that influence childhood health outcomes. We found that fungi are reliable biomarkers for gut maturation, with the notable emergence of Saccharomyces and Malassezia as some of the strongest indicators across both fungi and bacteria. Fungal composition was strongly associated with infant age (R = 0.79, p < 0.001) and with the later development of both atopic dermatitis (adj. p = 0.029) and food allergy (adj. p = 0.013). Further, differences in fungal development coincided with changes in key gut immune-modulating metabolites such as butyrate and glycerol, indicating the functional importance of infant gut mycobiome maturation in early-life immune development. Together, these results highlight the early life mycobiome as a potential therapeutic target to mitigate allergic disease development.},
}

Humans
*Malassezia/genetics/isolation & purification/physiology
Infant
Feces/microbiology
*Dermatitis, Atopic/microbiology/immunology
*Gastrointestinal Microbiome/genetics
Mycobiome
Male
Female
Child, Preschool
*Food Hypersensitivity/microbiology/immunology
Child
Metagenome
Metagenomics
*Hypersensitivity/microbiology

@article {pmid42337676,
year = {2026},
author = {Gorji, AE and Xue, B and Yan, T and Sadkowski, T and Chen, X and Cristobal-Carballo, O and Morrison, S and Razban, V and Smith, L and Stergiadis, S and Theodoridou, K and Shirali, M},
title = {Apple pomace and hempseed cake can reduce methane intensity (CH4/DMI) and alter the rumen microbiome in dairy cows: a shotgun metagenomic approach.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42337676},
issn = {1674-9782},
support = {Project No. 21/5/01//Department of Agriculture, Environment and Rural Affairs (DAERA)/ ; },
abstract = {BACKGROUND: With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows.

METHODS: Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes.

RESULTS: Values are reported as mean ± SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7% ± 2.8%, P = 0.032; HC: 54.5% ± 3.4%, P = 0.048) compared to the Control (48.2% ± 3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81 ± 0.06 (Control) to 0.58 ± 0.05 for AP (P = 0.012) and 0.64 ± 0.05 for HC (P = 0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P < 0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways (P = 0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P = 0.0075) and methane emissions per unit of dry matter intake (CH4/DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P = 0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P = 0.035), alongside a significant reduction in methane intensity (CH4/DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments (P > 0.05).

CONCLUSIONS: In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.},
}

@article {pmid42338488,
year = {2026},
author = {Chen, B and Chen, J and Feng, Z and Lv, H and Lin, Q and Jiang, G},
title = {Gut microbiota reconstruction after liver transplantation and its association with early postoperative infections in patients with liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1845273},
pmid = {42338488},
issn = {2235-2988},
mesh = {Humans ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Retrospective Studies ; *Postoperative Complications/microbiology ; Dysbiosis/microbiology ; Male ; *Liver Failure/surgery/complications ; Probiotics/administration & dosage/therapeutic use ; Middle Aged ; Metagenomics ; Feces/microbiology ; Adult ; *Bacterial Infections/microbiology/epidemiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Postoperative infection remains a major cause of morbidity after liver transplantation (LT) in patients with liver failure. Increasing evidence suggests that gut microbiota dysbiosis may contribute to infection risk, but its dynamic changes after LT are not fully understood.

METHODS: This retrospective study included 60 patients with liver failure who underwent LT and developed postoperative infection-related risk. Patients were divided into a probiotic group and a non-probiotic group. Fecal samples were collected before transplantation and on postoperative days 7, 14, 21, and 28. Metagenomic sequencing was performed to analyze gut microbial composition, diversity, and antibiotic resistance genes.

RESULTS: The probiotic group showed a significantly lower rate of postoperative bacterial infection, especially intra-abdominal infection. After LT, gut microbiota gradually recovered in both groups, but restoration was faster in the probiotic group. The non-probiotic group showed persistent dysbiosis, characterized by enrichment of opportunistic pathogens such as Enterococcus and Klebsiella, whereas beneficial genera including Bifidobacterium and Lactobacillus were more abundant in the probiotic group. Antibiotic resistance genes were also more enriched in the non-probiotic group.

CONCLUSION: Early postoperative gut microbiota reconstruction is closely associated with infectious complications after LT, and modulation of gut microbiota may help improve postoperative outcomes.},
}

Humans
*Liver Transplantation/adverse effects
Female
*Gastrointestinal Microbiome
Retrospective Studies
*Postoperative Complications/microbiology
Dysbiosis/microbiology
Male
*Liver Failure/surgery/complications
Probiotics/administration & dosage/therapeutic use
Middle Aged
Metagenomics
Feces/microbiology
Adult
*Bacterial Infections/microbiology/epidemiology
Bacteria/classification/genetics/isolation & purification

@article {pmid42338489,
year = {2026},
author = {Tang, C and Li, B and Chen, J and Liu, X and She, C},
title = {Causal relationship between gut microbiota and adenomyosis: metagenomics sequencing and Mendelian randomization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1772864},
pmid = {42338489},
issn = {2235-2988},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Adenomyosis/microbiology/etiology ; *Mendelian Randomization Analysis ; *Metagenomics/methods ; Middle Aged ; Adult ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in the pathogenesis of adenomyosis (AM); however, whether this association is causal and through which mechanisms it operates remain largely unknown.

METHODS: To interrogate potential causal relationships, we performed a two-sample Mendelian randomization (MR) analysis leveraging inverse-variance weighting (IVW) as the primary estimator, complemented by MR-Egger, weighted median, and weighted mode approaches, to evaluate the causal effects of gut microbial taxa and microbiota-derived metabolic pathways on AM. We further conducted mediation analyzes to delineate the role of circulating immune-cell phenotypes in this process. In parallel, in an independent clinical cohort, 22 patients with AM and 23 age-matched healthy controls recruited from the health-screening center of our institution were enrolled according to stringent inclusion and exclusion criteria (including antibiotic-use history and long-term local residency) and subjected to shotgun metagenomic sequencing. Significant differences in the types of bacterial communities were observed between the AM group and the control group. Subsequently, the results were cross-compared with those of the MR study using the Linear Discriminant Analysis Effect Size (LEfSe) method, and further verified using the ANCOM-BC method to determine the common microbial characteristics.

RESULTS: MR analysis identified ten microbial taxa and ten metabolic pathways with evidence of potential causal associations with AM. Of these, nine taxa and five pathways were associated with a reduced risk of AM, including Alistipes indistinctus (OR = 0.847, 95% CI = 0.754-0.951, p = 0.005, p~FDR~ > 0.05), Ruminococcus torques (OR = 0.818, 95% CI = 0.712-0.941, p = 0.005, p~FDR~ > 0.05), class Deltaproteobacteria (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), family Desulfovibrionaceae (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), order Desulfovibrionales (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), Parasutterella excrementihominis (OR = 0.875, 95% CI = 0.784-0.977, p = 0.017, p~FDR~ > 0.05), Ruminococcus bromii (OR = 0.836, 95% CI = 0.718-0.972, p = 0.020, p~FDR~ > 0.05), Bacteroides finegoldii (OR = 0.919, 95% CI = 0.855-0.987, p = 0.020, p~FDR~ > 0.05), and the genus Parasutterella (OR = 0.886, 95% CI = 0.797-0.986, p = 0.026, p~FDR~ > 0.05); the five protective pathways comprised dTDP-L-rhamnose biosynthesis (OR = 0.819, 95% CI = 0.674-0.995, p = 0.045, p~FDR~ > 0.05), lactose and galactose degradation (OR = 0.818, 95% CI = 0.689-0.972, p = 0.022, p~FDR~ > 0.05), the reductive TCA cycle (OR = 0.919, 95% CI = 0.851-0.993, p = 0.032, p~FDR~ > 0.05), allantoin degradation to glyoxylate (OR = 0.907, 95% CI = 0.830-0.991, p = 0.030, p~FDR~ > 0.05), and glycolysis I (from glucose-6-phosphate) (OR = 0.850, 95% CI = 0.747-0.967, p = 0.013, p~FDR~ > 0.05).Conversely, one taxon and five pathways were associated with an increased risk of AM: the genus Lactobacillus (OR = 1.083, 95% CI = 1.008-1.164, p = 0.030, p~FDR~ > 0.05), degradation of glucose and glucose-1-phosphate (OR = 1.202, 95% CI = 1.056-1.369, p = 0.005, p~FDR~ > 0.05), peptidoglycan biosynthesis (in Enterococcus faecium) (OR = 1.138, 95% CI = 1.007-1.285, p = 0.039, p~FDR~ > 0.05), pyruvate fermentation to acetone (OR = 1.118, 95% CI = 1.001-1.248, p = 0.048, p~FDR~ > 0.05), glycerol degradation to butanol (OR = 1.118, 95% CI = 1.011-1.237, p = 0.031, p~FDR~ > 0.05), and de novo pyrimidine deoxyribonucleotide biosynthesis (OR = 1.216, 95% CI = 1.063-1.390, p = 0.004, p~FDR~ > 0.05).Mediation analysis revealed that the immune phenotype "CD24 on CD24[+]CD27[+] B cells" mediated the pathway from Ruminococcus bromii to AM, accounting for 32.91% of the total effect (p = 0.020).Shotgun metagenomic profiling of the clinical cohort demonstrated no significant differences in α-diversity or β-diversity between the AM and control groups. At the phylum level, the relative abundance of Desulfobacterota was significantly decreased in the AM group (p< 0.05), and at the genus level, Alistipes was similarly reduced (p< 0.05). LEfSe analysis further indicated enrichment of Escherichia and Clostridium in the AM group, whereas Desulfobacterota and Rikenellaceae were enriched in the Control group. Matching the aforementioned results with the Mendelian randomization (MR) outcomes revealed that Desulfovibrionales and Desulfovibrionaceae constituted the shared microbial taxa. This finding was subsequently re-validated and confirmed using the ANCOM-BC method.

CONCLUSIONS: Integrating genetic causal inference with clinical metagenomic validation, this study provides convergent evidence that specific gut microbial taxa, their associated metabolic pathways, and immune-cell-mediated mechanisms may be causally implicated in the development of AM. These findings offer a framework for future microbiota-targeted preventive and therapeutic strategies against AM.},
}

Humans
Female
*Gastrointestinal Microbiome/genetics
*Adenomyosis/microbiology/etiology
*Mendelian Randomization Analysis
*Metagenomics/methods
Middle Aged
Adult
Bacteria/classification/genetics

@article {pmid42338795,
year = {2026},
author = {Chen, J and Wei, J and Liu, T and Chen, J and Yuan, Y and Zhang, F and Zhang, J},
title = {Gut microbiome dynamics in autism: a prospective nested case-control study demonstrates microbial-clinical associations following rehabilitation interventions.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1820904},
pmid = {42338795},
issn = {1662-4548},
abstract = {BACKGROUND: Children with autism spectrum disorder (ASD) commonly exhibit gut microbiota dysbiosis and metabolic abnormalities, yet the mechanisms linking these changes to clinical symptoms remain unclear.

OBJECTIVE: This study employed a nested case-control design and multi-omics approaches to evaluate the effects of rehabilitation intervention on clinical symptoms and gut microbiota in children with ASD, identify distinct microbial-metabolic signatures, and explore their mechanistic links with sleep disorders and developmental abilities.

METHODS: Within a prospectively established pediatric cohort (n = 45), we implemented a nested case-control design including 26 ASD children (18 males, 8 females; mean age 61.79 ± 11.15 months) and 19 age- and sex-matched healthy controls. All ASD participants received standardized rehabilitation therapy (2 h/day, 5 days/week for 6 months) comprising occupational therapy and cognitive-linguistic training. Primary outcomes included comprehensive clinical assessments [Griffiths Development Scales-Chinese (GDS-C), Children's Sleep Habits Questionnaire (CSHQ), Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS)] and longitudinal multi-omics analysis (metagenomic sequencing and LC-MS-based metabolomics). Association analyses were performed with FDR correction (q < 0.05).

RESULTS: Following the 6-month rehabilitation intervention, significant clinical improvements were observed in sleep quality (CSHQ total and subscores) and developmental performance (GDS-C). Multi-omics profiling revealed distinct biological signatures in ASD children compared to healthy controls, characterized by elevated Intestinibacter_bartlettii and reduced levels of ornithine and siderophore nonribosomal peptide biosynthesis. Crucially, correlation analysis demonstrated that, after FDR correction, ornithine levels were significantly positively correlated with multiple GDS-C developmental domains, while tyrosine was associated with parasomnias. These findings establish a potential mechanistic link where amino acid metabolism connects gut microbial shifts to clinical phenotypes.

CONCLUSION: This study demonstrates that rehabilitation intervention synchronously ameliorates clinical symptoms and modulates the gut-metabolic profile in ASD. The identified associations between specific metabolites (ornithine and tyrosine) and clinical outcomes suggest a metabolic mechanism underlying the gut-brain axis, highlighting the potential of these metabolites as biomarkers for therapeutic monitoring. Further large-scale studies are needed to validate these findings.},
}

@article {pmid42338857,
year = {2026},
author = {Baumgartner, EE and Weltin, L and Whitten, JP and Fahey, TE and Baumgartel, PB and Farrell, JJ},
title = {An Unusual Infectious Cause of Abdominal Pain: Non-typhoidal Salmonella Aortitis Complicating an Endovascular Aortic Stent Graft.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109509},
pmid = {42338857},
issn = {2168-8184},
abstract = {Non-typhoidal Salmonella (NTS) is a rare but life-threatening cause of infectious aortitis and mycotic aneurysm formation, predominantly affecting immunocompromised patients and those with pre-existing vascular pathology or prosthetic hardware. Diagnosis is frequently delayed due to its non-specific clinical presentation and the poor sensitivity of conventional blood cultures. A 73-year-old immunocompromised woman with a history of penetrating aortic ulcer and prior endovascular aortic stent graft placement presented with progressive abdominal pain and para-aortic soft tissue thickening encasing the infrarenal aorta. Blood cultures were negative; however, CT-guided peri-aortic tissue aspiration and metagenomic next-generation sequencing (mNGS; Karius test) identified Salmonella enterica serovar Enteritidis susceptible to ampicillin, ceftriaxone, levofloxacin, nalidixic acid, and trimethoprim/sulfamethoxazole. The most probable infection source was the patient's prolonged daily consumption of unpasteurized eggs from backyard chickens. She was treated with intravenous (IV) ceftriaxone for 30 days followed by 18 months of oral cephalexin suppression, with significant radiographic improvement at three-month follow-up. Surgical intervention was deferred given her high operative risk from metastatic malignancy and multiple comorbidities. This case is notable for its documentation of culture-negative NTS aortitis complicating an endovascular stent graft, in which mNGS was essential for pathogen identification. It further highlights the importance of eliciting detailed dietary exposure history in high-risk patients, the novel diagnostic challenge posed by concurrent autoimmune disease mimicking non-infectious vasculitis, and the feasibility of antibiotic-only management in carefully selected surgical non-candidates.},
}

@article {pmid42338881,
year = {2026},
author = {Wang, H and Wang, Y and Yang, L and Feng, J and Tian, S and Chen, L and Huang, W and Liu, J and Wang, X},
title = {Correction: Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852209},
doi = {10.3389/fmicb.2026.1852209},
pmid = {42338881},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1375804.].},
}

@article {pmid42338883,
year = {2026},
author = {Goktas, NT and Guven, S and Dinleyici, EC},
title = {The combination of Lactobacillus acidophilus DSMZ 26280 and Limosilactobacillus reuteri DSMZ 25441 has an impact on clinical course and gut microbiota of children with acute infectious diarrhea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1792126},
pmid = {42338883},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous studies and society guidelines have proposed probiotics as a complementary therapy for acute infectious diarrhea, which may shorten the disease course, yet strain-specific effects and microbiome correlates remain incompletely defined. We aim to evaluate the effect of a combination of Lactobacillus acidophilus and Limosilactobacillus reuteri on the duration of diarrhea and gut microbiota composition in children with acute infectious diarrhea.

PATIENT AND METHODS: In a prospective, randomized, controlled, open-label trial at a tertiary pediatric emergency department (March-August 2024), children aged 1-6 years with acute infectious diarrhea lasting less than 24 h were allocated 1:1 to standard therapy (oral rehydration ± intravenous fluids) with or without 5-day probiotic (L. acidophilus DSMZ 26280; 108 CFU) and (L. reuteri DSMZ 25441; 108 CFU). Primary outcomes were duration of diarrhea and the proportion diarrhea-free at 72 h. The secondary outcome measures included the proportion of diarrhea-free children during first 10th day of the study. A subgroup analysis for gut microbiota composition at Day 0, 10th and 30th days of the study have been performed.

RESULTS: Of 145 enrolled children, 79 in the probiotic group (34 girls, 45 boys) and 66 in the control (30 girls and 36 boys); baseline demographics were comparable. The duration of diarrhea was significantly reduced in the probiotic group compared to the control group (46.4 ± 29.6 h vs. 81.6 ± 38.5 h, p < 0.001). The percentage of diarrhea-free children was significantly larger in the probiotic group at 72 h compared to the control (86.0% vs. 33.3%, p < 0.001). Persistence of diarrhea was lower in the probiotic group at 24, 48, and 96 h (all p < 0.001) and at day 6 (2.5% vs. 15.1%; p < 0.05); by days 7-10, persistence was rare in both groups. The probiotic combination is well-tolerated, and no adverse events have been reported. Alpha diversity indices were unchanged within/between groups. Bray-Curtis and Jaccard PCoA showed no between-group separation; unweighted UniFrac revealed differences within the probiotic group (day 1 vs. day 30) and between groups at day 30 (p < 0.05). LEfSe indicated enrichment of taxa associated with recovery in the probiotic arm and control group, and there is difference between group at Day 30.

CONCLUSION: This study evaluates a specific combination of L. acidophilus DSMZ 26280 and L. reuteri DSMZ 25441 in a randomized controlled setting, adding to the growing body of strain-specific probiotic research in pediatric acute infectious diarrhea. Adding probiotics to treatment is well-tolerated and reduces the duration of diarrhea by approximately 35 h when it starts in the early hours of infection. This probiotic combination use is associated with modest phylogenetics shifts in gut microbiota composition, with enrichment of certain taxa that have been previously associated with gut homeostasis in other contexts; however, their functional and clinical significance in this setting remains unclear. Larger blinded trials are warranted to confirm durability and detailed metagenomic analysis including metabolomics.},
}

@article {pmid42338911,
year = {2026},
author = {Huang, Y and Chen, F and Yu, Z and Sheng, X and Wen, S and Zhang, X and Tang, W and Huang, M},
title = {Integrated analysis of physicochemical properties, microbiome, and flavor profiles for differentiating two aroma grades of sauce-flavor Daqu.},
journal = {Food chemistry: X},
volume = {37},
number = {},
pages = {104092},
pmid = {42338911},
issn = {2590-1575},
abstract = {Aroma characteristics are critical indicators for evaluating sauce-flavor Daqu quality. This study systematically compared physicochemical properties, enzyme activities, microbiomes, and flavor profiles of first-grade (GF) and second-grade (GS) aroma Daqu. GF had higher total acidity, amino nitrogen content, acid protease activity, a lower pH, and was correlated with enrichment of bacteria potentially associated with flavor precursor production such as Kroppenstedtia guangzhouensis and Kroppenstedtia eburnea. GS showed higher liquefying/cellulase activities and pH, and was associated with dominance by hydrolytic fungi such as Paecilomyces variotii and off-odor-related Oceanobacillus. HS-SPME-GC-MS combined with VIP and OAV analyses identified 11 differential volatile compounds. Aldehydes were strongly correlated with positive aroma grading and may serve as potential indicators associated with grade differentiation, while GS accumulated dimethyl trisulfide correlating with off-odors. The findings reveal the relationships between multi-omics characteristics and aroma grade differentiation of Daqu, and provide theoretical support for Daqu quality evaluation and production regulation.},
}

@article {pmid42338938,
year = {2026},
author = {Zhong, L and Xia, K and Fan, Y},
title = {Sigmoid colonic tuberculosis presenting as a colovesical fistula mimicking colorectal malignancy: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1857599},
pmid = {42338938},
issn = {2296-858X},
abstract = {BACKGROUND: Intestinal tuberculosis (ITB) most commonly involves the ileocecal region. Isolated sigmoid colonic tuberculosis complicated by a colovesical fistula is extremely rare and may closely mimic colorectal malignancy or Crohn's disease (CD).

CASE PRESENTATION: A 73-year-old man presented with subacute diarrhea, fever, and lower urinary tract symptoms. Laboratory tests showed markedly elevated inflammatory markers and anemia. Cross-sectional imaging demonstrated segmental thickening of the sigmoid colon, pericolic lymphadenopathy, multiple serous effusions, and findings consistent with a colovesical fistula, including bladder wall disruption and intravesical gas. Colonoscopy revealed a circumferential stenosing lesion with irregular ulceration, raising strong suspicion for colorectal malignancy or CD.

Initial histopathology showed only mixed inflammatory cell infiltration without granulomas or malignant cells, and empirical antimicrobial therapy failed to control the fever. Given the positive immunological testing for tuberculosis and persistent clinical suspicion, acid-fast bacilli staining and metagenomic next-generation sequencing (mNGS) were performed on colonic biopsy tissue. Acid-fast bacilli were detected, and mNGS identified Mycobacterium tuberculosis complex, confirming ITB. Standard anti-tuberculosis therapy was initiated, leading to rapid clinical improvement, complete endoscopic mucosal healing, and radiological resolution of the colovesical fistula.

CONCLUSION: This case highlights that ITB can present as an isolated tumor-like sigmoid lesion complicated by fistula formation. When routine histology is nondiagnostic, especially in the absence of granulomas, integration of imaging, immunological testing, special staining, and molecular diagnostics may be crucial for early diagnosis, avoidance of misdiagnosis, and timely targeted treatment.},
}

@article {pmid42339070,
year = {2026},
author = {Happi, AN and Ogunsanya, OA and Sijuwola, AE and Saibu, FM and Akano, K and Ayinla, AO and Daodu, RO and Page, B and Olumade, TJ and Oguzie, JU and Oluniyi, PE and Adedokun, OA and Fadele, J and Nwofoke, C and Elias, OT and Ogundana, KE and Lawal, OZ and Nosamiefan, I and Okolie, J and Adelabu, A and Lombardi, K and Eller, LA and Broach, E and Prins, PA and Heeney, JL and Modjarrad, K and Njatou, TLFA and Parker, ZF and McCauley, M and Vasan, S and Parker, E and Collins, ND and Michael, NL and Happi, CT},
title = {Genomic epidemiology and evolutionary analysis of Lassa virus from small mammals suggest bidirectional viral movement across humans and animals.},
journal = {Virus evolution},
volume = {12},
number = {1},
pages = {veag032},
pmid = {42339070},
issn = {2057-1577},
abstract = {Lassa fever is a viral haemorrhagic fever that poses a persistent public health threat in several West African countries, particularly Nigeria. The scarcity of Lassa virus (LASV) sequences isolated from small mammal reservoirs limits our knowledge and understanding of LASV genomic diversity and transmission dynamics. To address this knowledge gap, we sampled 1189 small mammals, including mice, rats, and shrews, from two LASV-endemic states in southern Nigeria (Ondo and Ebonyi States) and tested them for the presence of LASV RNA using reverse transcription-quantitative polymerase chain reaction. Selected quantitative polymerase chain reaction-positive samples were subjected to whole genome sequencing and small mammal speciation through next-generation sequencing outputs. We recorded an overall polymerase chain reaction positivity rate of 61.6%, with rat species demonstrating the highest LASV prevalence. We also conducted a serosurvey of 269 small rodents using indirect Enzyme-Linked Immunosorbent Assay (ELISA) and obtained an overall anti-LASV seroprevalence of 45%. Using the Nextera XT metagenomic sequencing protocol, we produced 55 LASV partial (n = 28) and full-length genomes (n = 27) from small mammals sampled, all of which clustered within sublineage 2g. LASV sequences generated from this study suggest that LASV variation is mostly driven by location, as isolates from this study tend to cluster more closely with other isolates collected from within the same region, rather than by collection date or host. However, samples collected from Ebonyi State were more closely related to isolates collected in Ondo State than to isolates from Edo, despite a larger physical distance. Overall, the data from this study suggest free movement of the virus across states in Nigeria, among humans and various non-human taxa. The finding of LASV in additional small mammal hosts suggests that the virus reservoir is vast and may include many small mammals not well-characterized.},
}

@article {pmid42339199,
year = {2026},
author = {Acosta-España, JD and Altamirano-Jara, JB and Herrera-Yela, A and Estrella, F and Palacios, S},
title = {Metagenomic identification of Acanthamoeba Rhysodes in chronic skin lesion: Case report and literature review.},
journal = {JAAD case reports},
volume = {73},
number = {},
pages = {160-164},
pmid = {42339199},
issn = {2352-5126},
}

@article {pmid42339286,
year = {2026},
author = {Dang, Y and Kong, J},
title = {A double pathogen strike: COVID-19 and talaromycosis Co-infection in a patient with post-tuberculosis lung disease.},
journal = {Respiratory medicine case reports},
volume = {62},
number = {},
pages = {102450},
pmid = {42339286},
issn = {2213-0071},
abstract = {An 80-year-old woman from rural Guangxi with post-tuberculosis lung disease (PTLD) (hereinafter referred to as PTLD)presented with one month of cough and fever. One month prior, she had ingested raw rodent meat-a known exposure for Talaromyces marneffei. Chest HRCT showed bilateral tree-in-bud opacities superimposed on prior left lung destruction. Conventional microbiological tests, including acid-fast bacilli smears, were negative. A nasopharyngeal swab was positive for SARS-CoV-2 (cycle threshold 17). Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified both T. marneffei and SARS-CoV-2. Her CD4[+] count was 344/μL and HIV serology was negative. She received nirmatrelvir-ritonavir and sequential amphotericin B followed by voriconazole, with clinical and radiological improvement. This case illustrates that PTLD may serve as a local anatomical risk factor for talaromycosis even without systemic immunodeficiency.},
}

@article {pmid42339375,
year = {2026},
author = {Tomasi, N and Banchi, E and Manna, V and Celussi, M},
title = {Surface sediments prokaryotic communities: five years of 16S rRNA amplicon sequencing data from the northernmost part of the Mediterranean Sea.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112971},
pmid = {42339375},
issn = {2352-3409},
abstract = {Surface sediments harbour diverse prokaryotic communities that play a key role in biogeochemical cycling and provide valuable insights when compared with water column communities, allowing for a more comprehensive understanding of marine ecosystem functioning. Specifically, this dataset presents prokaryotic community data from 16 surface sediment samples collected seasonally from June 2020 to May 2025 at the C1-LTER station (45°42'2.99″ N, 13°42'36.00″ E; DEIMS.iDhttps://deims.org/96969205-cfdf-41d8-979f-ff881ea8dc8b) in the Gulf of Trieste, located in the northeastern Adriatic Sea (Mediterranean Sea). Extracted DNA was sequenced following the 16S Metagenomic Sequencing Library Preparation protocol and run on an Illumina NovaSeq 6000 System. Raw reads were filtered and denoised with DADA2, and taxonomic assignment was performed against the Silva 138.2 99% reference database. The dataset provides useful insights into prokaryotic communities and their seasonal variability over five years. Moreover, a focus on specific taxa is provided, such as Cyanobacteriota and Archaea, highlighting patterns of community variability in the sediment. Finally, it shows seasonal stability and generally consistent taxa distribution over time, as indicated by the high proportion of shared taxa at each taxonomic level. The raw data, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1442017, include two sets of sequencing reads obtained from surface sediment samples using the Illumina MiSeq and Illumina NovaSeq 6000 sequencing platforms, for a total of 27 16S rRNA gene sequencing FASTQ files. Overall, these data provide valuable insight into the surface sediment community in the northernmost part of the Mediterranean Sea, contributing to long-term research on sediment prokaryotic communities.},
}

@article {pmid42339699,
year = {2026},
author = {Patel, D and Heidenblut, M and Mau, RL and Wagner, WP and Schwartz, E and Dijkstra, P and Hungate, BA and Ceja-Navarro, JA},
title = {Protist Predation Rapidly Reshapes Soil Microbial Gene Expression Linked to Nutrient Processing, Resistance, Virulence, and Gene Mobility Traits.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18948},
pmid = {42339699},
issn = {1520-5851},
abstract = {Protists are ubiquitous soil predators that regulate bacterial communities and biogeochemical cycling, yet how their predation alters expression of nutrient-cycling genes and traits linked to antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in natural soils remains poorly understood. Here, we used a short-term soil microcosm experiment to distinguish the effects of moisture-stimulated resident protists from enhanced predation by an introduced exogenous predatory protist community. Using quantitative stable isotope probing (qSIP) and metagenomic and metatranscriptomic analyses, we tracked protist activity and microbial responses over 3 days. Enhanced predation rapidly reshaped transcriptionally active microbial communities, increasing expression of nitrogen and phosphorus cycling genes while concurrently elevating diversity and transcription of ARGs, VFs, and MGEs, including multidrug-efflux systems, motility-, biofilm-related traits, and phage-associated elements. Metagenome-assembled genome─resolved analyses showed that some resident soil populations were activated by wet-up and remained transcriptionally active under predation pressure, encoding nutrient-cycling, resistance, virulence, and mobility traits that contributed to the functional background of wetted soils. These results suggest that, even over short time periods, protist predation links soil nutrient processing with environmentally relevant resistance and genetic mobility pathways, acting as a crucial ecological driver of gene expression related to nutrient processing and microbial interaction traits during environmental change.},
}

@article {pmid42340399,
year = {2026},
author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA},
title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02818-y},
pmid = {42340399},
issn = {1432-184X},
abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.},
}

@article {pmid42341025,
year = {2026},
author = {Wohl, DL and Belder, PT and Mitchell, BD},
title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350558},
doi = {10.1371/journal.pone.0350558},
pmid = {42341025},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; },
abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Saliva/microbiology
*Amish
Female
Male
Oral Health
Adult
Middle Aged
Dental Plaque/microbiology
Bacteria/genetics/classification

@article {pmid42341423,
year = {2026},
author = {Zheng, J and Yao, DY and Lu, YY and Luo, SJ and Liang, XX},
title = {Diagnostic utility of metagenomic next-generation sequencing for determining the etiology of thoracolumbar spine infections.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117517},
doi = {10.1016/j.diagmicrobio.2026.117517},
pmid = {42341423},
issn = {1879-0070},
abstract = {OBJECTIVE: This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) in identifying the etiological agents of thoracolumbar spine infections and examined its clinical relevance in facilitating timely diagnosis and therapeutic decision-making.

METHODS: A total of 54 patients with suspected thoracolumbar spinal infection admitted to the Department of Spinal Orthopedics between June 1, 2022, and January 15, 2026, were enrolled. Tissue specimens from all patients underwent microbial culture, histopathological examination, and metagenomic next-generation sequencing (mNGS). Based on established clinical diagnostic criteria, patients were classified into an infection group (n = 49) and a non-infection group (n = 5). The pathogen detection rate, and diagnostic sensitivity of mNGS and conventional culture were compared using the paired χ² test.

RESULTS: Among the 54 patients with suspected thoracolumbar spine infection, the male-to-female ratio was 2:1. The overall positive detection rate of mNGS was 75.9% (41/54), which was significantly higher than that of microbial culture at 57.4% (31/54) (χ² = 4.500, p < 0.05). When clinical diagnosis served as the reference standard, mNGS demonstrated greater sensitivity for diagnosing thoracolumbar spinal infections compared to microbial culture (83.7% vs. 63.3%), and this difference reached statistical significance (χ² = 4.500, p < 0.05).

CONCLUSION: mNGS shows a high pathogen detection rate and superior sensitivity for diagnosing thoracolumbar spinal infection, providing valuable support for clinical diagnosis and guiding therapeutic management in suspected cases.},
}

@article {pmid42341424,
year = {2026},
author = {Tsuboi, I and Inoue, S and Hirayama, T and Mitsui, Y and Watanabe, M and Hirakawa, H and Sadahira, T},
title = {Gut, vaginal, and urinary microbiome alterations in women with genitourinary syndrome of menopause: A systematic review.},
journal = {Maturitas},
volume = {211},
number = {},
pages = {109031},
doi = {10.1016/j.maturitas.2026.109031},
pmid = {42341424},
issn = {1873-4111},
abstract = {BACKGROUND AND OBJECTIVE: Genitourinary syndrome of menopause (GSM) is a chronic condition caused by estrogen deficiency, encompassing vaginal dryness, dyspareunia, and urinary symptoms. Alterations in the vaginal, urinary, and gut microbiome may contribute to GSM pathophysiology. We synthesize the evidence on microbiome composition and diversity across these compartments in postmenopausal women with GSM.

METHODS: PubMed, Scopus, and Embase were searched from inception to April 2026 for studies assessing the microbiome in postmenopausal women with GSM using 16S rRNA gene sequencing, metagenomics, or culture-based methods.

RESULTS: Twenty-three studies (5027 participants) were included: 15 examined the vaginal microbiome, seven the urinary microbiome, and one the gut microbiome. Postmenopausal women consistently showed reduced Lactobacillus abundance and increased microbial diversity. Estrogen therapy partially restored Lactobacillus dominance but did not uniformly improve symptoms. In the SWAN cohort (n = 1320), sexual pain was the only GSM symptom independently associated with a specific community state type (CST IV-C1; OR 2.26, 95% CI 1.20-4.23). Specific species showed associations with distinct symptom domains: Prevotella with urinary symptoms, Finegoldia magna with recurrent urinary tract infection, and Streptococcus with sexual pain. Parallel Lactobacillus depletion and pathobiont enrichment across all three compartments pointed toward a vaginal-bladder-gut axis, potentially linked through estrobolome disruption and bacterial translocation.

CONCLUSION: The postmenopausal genitourinary microbiome is characterized by Lactobacillus depletion and increased diversity, but microbiome restoration alone does not predict symptom resolution. The shared microbial alterations across compartments suggest a vaginal-bladder-gut axis that may collectively drive GSM, but this requires multi-compartment longitudinal validation. PROSPERO registration: CRD420261335478.},
}

@article {pmid42341530,
year = {2026},
author = {Lu, B and Wang, P and Hu, J and Qian, J and Shen, J and Tang, S and Zong, Y},
title = {Aqueous PFOS exposure decouples gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {406},
number = {},
pages = {128638},
doi = {10.1016/j.envpol.2026.128638},
pmid = {42341530},
issn = {1873-6424},
abstract = {Wetland interfaces regulate greenhouse-gas exchange and carbon retention, yet contaminant exposure may disrupt the relationship between these two processes. Whether aqueous perfluorooctane sulfonate (PFOS), a persistent aquatic contaminant, alters this relationship remains unclear. Here, we used a controlled rhizobox mesocosm with paired planted and unplanted treatments across an aqueous PFOS gradient (0, 10, 100, and 1000 μg L[-1]) to resolve plant-mediated and background soil responses. We combined endpoint, time-weighted 24-h CO2 and CH4 flux partitioning with [13]CO2 tracing of root-derived carbon, rhizosphere priming estimates, soil organic carbon fractionation into particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and metagenomic profiling. PFOS induced clear exposure-dependent and non-linear responses. Low-to-medium PFOS stimulated root-associated CO2 fluxes and maintained positive rhizosphere priming, whereas high PFOS suppressed rhizosphere CO2 and root respiration, weakened net plant CO2 uptake, and shifted soil organic carbon priming to a net negative response. In contrast, at H-P, MAOC was significantly higher than the control in both bulk and rhizosphere compartments, indicating that mineral-associated carbon retention can persist even when biological carbon processing weakens. Metagenomic profiling further suggested compartment-specific microbial filtering, reduced genetic potential for polymer depolymerization, and reweighted methane-related functions under PFOS exposure. Together, these results show that aqueous PFOS exposure can decouple gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms. These findings indicate that lower gaseous carbon release under PFOS exposure should not be interpreted straightforwardly as stronger carbon-retention function or enhanced carbon sequestration, particularly without longer-term field validation.},
}

@article {pmid42341576,
year = {2026},
author = {Gupta, G and Fortin, RM and Labrie, S and Filteau, M},
title = {Genomic insights and antifungal potential of Pseudomonas species isolated from maple sap, including the novel species Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126738},
doi = {10.1016/j.syapm.2026.126738},
pmid = {42341576},
issn = {1618-0984},
abstract = {Fungal contamination poses a significant challenge in maple sap collection systems and postproduction processes, which affects the quality and shelf life of maple syrup. As an alternative to chemical treatments, microorganisms offer promising biocontrol potential. This study investigates nine Pseudomonas strains isolated from maple sap for their antifungal activity and genomic features. Whole-genome sequencing followed by comparative genomic analysis identified five distinct Pseudomonas species, including two previously uncharacterized taxa for which we propose the names Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov., in accordance with the nomenclatural guidelines of the SeqCode. Strain distributions from metagenome recruitment suggest they originate from sapwood, and previous metataxonomic data show that the amplicon sequence variant matching P. edsoni predominated maple sap samples. Genome mining using antiSMASH and BAGEL4 identified gene clusters associated with the synthesis of antifungal compounds, such as hydrogen cyanide, siderophores, cyclic lipopeptides, and ribosomally synthesized peptides. Antifungal assays demonstrated inhibitory activity against food spoilage fungi, with P. edsoni strains being active against Kluyveromyces lactis. The absence of activity in the cell-free supernatant and the presence of Type VI secretion systems in the genomes point toward contact-dependent mechanisms. Collectively, these findings reveal previously unrecognized taxonomic diversity and ecological specialization in maple sap-associated Pseudomonas, providing a basis for the rational development of Pseudomonas-based antifungal strategies in maple syrup production and quality control.},
}

@article {pmid42341885,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113373},
doi = {10.1016/j.diabres.2026.113373},
pmid = {42341885},
issn = {1872-8227},
abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).

METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.

RESULTS: Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).

CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

@article {pmid42341953,
year = {2026},
author = {Cao, S and Han, YC and Wang, XC and Chen, R and Xing, BS},
title = {Unraveling the short- and long-term effects of lignocellulosic pretreatment derivatives on the anaerobic co-digestion of corn straw and food waste: Digester performance, microbial community, and metabolic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135234},
doi = {10.1016/j.biortech.2026.135234},
pmid = {42341953},
issn = {1873-2976},
abstract = {Lignocellulosic pretreatment hydrolysates often contain inhibitory derivatives, particularly furan inhibitors (furfural and 5-hydroxymethylfurfural) and phenolic compounds, which can suppress anaerobic digestion. In this study, a CS/FW mesophilic AcoD system was investigated through short-term single- and mixed-inhibitor batch tests and long-term operation in two continuous stirred tank reactors (CSTRs), with mixed-inhibitor concentrations increased stepwise at fixed ratios. The results revealed that the maximum concentrations of furfural, phenol, and 5-hydroxymethylfurfural tolerated by the AcoD system were 100, 50, and 50 mg/L, respectively, in short-term batch tests, whereas during long-term operation, twofold greater concentrations in the same ratio were tolerated, leading to a 4.2 % increase in methane yield compared with that of the control. At high concentrations of 1000:500:500 mg/L, the hydrolysis, acidification, and methanogenesis rates were strongly suppressed. Furfural showed the strongest inhibition on polysaccharide and protein degradation, indicating that hydrolysis was the main affected stage during AcoD. Metagenomic analysis revealed that the relative abundance of Methanobacterium increased from 39.03 % to 69.50 %, indicating a selective microbial adaptation. In contrast, the overall abundance of genes involved in both acetoclastic and hydrogenotrophic methanogenesis decreased, suggesting a reduction in community-level methanogenic functional potential, which was consistent with the observed 97.4 % decline in methane yield. Meanwhile, the relative abundances of oxidative stress defense genes, katE (EC:1.11.1.6) and GPX (EC:1.11.1.9), in the test group increased by 10.2 % and 19.9 %, respectively, indicating enhanced antioxidant capacity of the microbial community. These findings provide insights into the management of inhibitor-rich pretreatment hydrolysates during AcoD of CS and FW.},
}

@article {pmid42342666,
year = {2026},
author = {Jia, X and Jiang, L and Gong, Y and Chu, X and Yu, W and Du, J and Zhang, J and Shang, X and Wang, P and Wang, J and Li, Y and Wang, Z and Zhou, R and Li, Z and Zhu, Y and Wu, B and Li, J and Yang, Q},
title = {Fusobacterium periodonticum promotes colorectal tumorigenesis via decanoic acid-driven neutrophil chemotaxis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74591-y},
pmid = {42342666},
issn = {2041-1723},
abstract = {Gut microbiota dysbiosis and immune dysregulation are closely associated with the development of colorectal cancer. Identifying the mechanistic links among specific microbial species, metabolites, and immune responses is crucial for uncovering novel insights into its pathogenesis. Here we show, through metagenomic and metabolomic analyses of clinical cohorts, that Fusobacterium periodonticum is significantly enriched in colorectal cancer patients and strongly correlated with elevated decanoic acid levels. Single-cell transcriptomic results further reveal tissue-specific neutrophil enrichment in colorectal cancer tissues, characterized by high CXCL8 expression and activation of neutrophil-related immune pathways. Cellular experiments demonstrate that decanoic acid induces late apoptosis/necrosis of neutrophils, enhances their chemotaxis through a pertussis toxin-sensitive G-protein-dependent mechanism, and upregulates genes involved in leukocyte migration and tumorigenesis. Mouse models further confirm that F. periodonticum colonization increases intestinal dysplasia and decanoic acid levels, and that decanoic acid intervention promotes tumor progression by facilitating neutrophil infiltration and modulating the local immune microenvironment. Our study reveals an important role of F. periodonticum in colorectal tumorigenesis via decanoic acid-medicated neutrophil chemotaxis, providing mechanistic insights into the pathogenesis of colorectal cancer.},
}

@article {pmid42342687,
year = {2026},
author = {Rubbab, B and Adenwalla, A and Spottiswoode, N and Haston, JC and Firmani, S and Singh, S and Rajaram, V and Ramos, J and Ali, IKM and Whittemore, B and Hanners, NW},
title = {Neurosurgical Biopsy and Resection for Diagnosis and Treatment of Balamuthia mandrillaris Amebic Encephalitis, United States.},
journal = {Emerging infectious diseases},
volume = {32},
number = {7},
pages = {},
doi = {10.3201/eid3207.260725},
pmid = {42342687},
issn = {1080-6059},
abstract = {We report a systematic case review of antemortem neurosurgical resections and biopsies and outcomes including new lesions after procedure and survival in Balamuthia mandrillaris granulomatous amebic encephalitis. The investigation was prompted by a 5-year-old patient in the southwestern United States who was treated with nitroxoline, the 2021 Centers for Disease Control and Prevention regimen, and underwent 2 resections; initial resection site recurrence and a new lesion after resection prompted the question whether complete resection versus biopsy is associated with better outcomes. We conducted a literature review and found no substantial difference between neurosurgical resection versus biopsy-only groups. Limitations include case review, number of cases, and incomplete data available. Additional analyses comparing neurosurgical outcomes with outcomes of those diagnosed via blood or cerebrospinal fluid and metagenomic next-generation sequencing might provide more definitive answers. This case and systematic review provide evidence that treatment with nitroxoline and neurosurgical resection could contribute to survival in Balamuthia encephalitis case-patients.},
}

@article {pmid42342731,
year = {2026},
author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H},
title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42342731},
issn = {2055-5008},
support = {100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 323134//Norges Forskningsråd/ ; 323134//Norges Forskningsråd/ ; },
mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.},
}

*Lignin/metabolism
Metagenomics
Xylans/metabolism
*Carboxylic Acids/metabolism
Anaerobiosis
Fermentation
Ethanol/metabolism
Metabolic Networks and Pathways
*Bacteria/metabolism/classification/genetics
Cellulose/metabolism
Microbial Consortia
Lactic Acid/metabolism
Acetic Acid/metabolism
Carbon Dioxide/metabolism

@article {pmid42342987,
year = {2026},
author = {Saw, JH and Shlafstein, MD and Pavloudi, C and Monsalve, N and Prescott, RD and Chain, PSG and Decho, AW and Donachie, SP},
title = {Amplicon and metagenomic data from fumarole-associated geothermal features of Hawai'i.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07734-x},
pmid = {42342987},
issn = {2052-4463},
support = {2442122//National Science Foundation/ ; 1711856//National Science Foundation/ ; LANLF59T//Office of the Chief Information Officer, U.S. Department of Energy/ ; 80NSSC18K1064/NASA/NASA/United States ; },
abstract = {The Hawaiian Islands are among the most geologically and volcanically active places on Earth. While the Hawaiian Archipelago is known for its animal and plant diversity, much less is known about microbial diversity in the area's diverse habitats. In this study, we focused on steam vent associated biofilms found on the most volcanically active island of Hawai'i, also known as the Big Island. From 46 samples from various biofilms and associated features around fumaroles emitting water steam, we generated amplicon and metagenomic sequences. This represents a total of 276 Gbp of raw sequencing data. From the shotgun metagenomic data, we constructed 363 non-redundant medium- to high-quality metagenome-assembled genomes (MAGs) that are at least 70% complete and with less than 5% contamination. Of these, ten MAGs belong in the domain Archaea, and 353 belong in the domain Bacteria. This dataset could provide valuable insights into microbial diversity and ecology around volcanic features in Hawai'i and elsewhere.},
}

@article {pmid42332682,
year = {2026},
author = {Zhu, Q and Duan, Q and Wang, F and Shao, ZJ and Hu, W and Bi, YK and Wang, X and Li, JL and Zhu, D and Lv, ZH and Yang, ZF and Yin, YR},
title = {Characterization of an alkali- and glucose-tolerant β-glucosidase from Karamay saline-alkali soil and its structural basis for glucose tolerance.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-026-01191-5},
pmid = {42332682},
issn = {1472-6750},
support = {32560004 and 32570003//National Natural Science Foundation of China/ ; 202501AU070181 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; XZ202501ZY0019//the Science and Technology Projects of the Xizang Autonomous Region/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; 2025DNS01//the Dali Prefecture Science and Technology Bureau/ ; },
abstract = {BACKGROUND: Industrial applications of β-glucosidases are often constrained by high salinity, alkaline conditions, and glucose inhibition.

RESULTS: A glycoside hydrolase family 1 β-glucosidase, B0-BG40, was mined from the metagenome of saline-alkali soil in Karamay, Xinjiang, China. When heterologously expressed in Escherichia coli, B0-BG40 exhibited optimal activity at 45 °C and pH 8.6, retaining > 60% of its maximal activity over 20-55 °C and pH 5.6-9.6. The enzyme was highly stable at 25 °C, 40 °C and 45 °C and under alkaline conditions, maintaining > 85% residual activity after prolonged incubation and showing activity enhancement following incubation at pH 8.0-10.0. B0-BG40 also tolerated up to 2.0 M NaCl and 4.0 M glucose, and displayed weak glucose inhibition (Ki = 1033.5 mM). Combined with the results of protein homology modeling and molecular docking, a reasonable mechanistic hypothesis was proposed: the excellent glucose tolerance of the enzyme may be related to its narrow and deeply recessed catalytic channel, and this special channel structure could hinder glucose molecules from entering the active site.

CONCLUSIONS: B0-BG40 is a salt-, alkali-, and glucose-tolerant β-glucosidase with strong potential for applications in food and feed processing and cellulosic ethanol production.},
}

@article {pmid42332773,
year = {2026},
author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q},
title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-026-05012-6},
pmid = {42332773},
issn = {1741-7015},
support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.

METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.

RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles = 1.82; 95%CI = 1.17-2.81; p-trend = 0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction = 0.01). Similar interactions were seen for total fiber (p = 0.09), soluble fiber (p = 0.09), and insoluble fiber (p = 0.11), without statistical significance.

CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.},
}

@article {pmid42333020,
year = {2026},
author = {Habiba, MU and Rahman, MM and Augustin, MA and Varela, C and Morris, H and Bozkurt, H},
title = {Traditional Fermented Dairy Products as Reservoirs of Bifidobacterium With Probiotic Potential: From Microbial Diversity to Functional Characterization.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {4},
pages = {e70540},
doi = {10.1111/1541-4337.70540},
pmid = {42333020},
issn = {1541-4337},
support = {//Adelaide University/ ; //University of Adelaide Research Scholarship/ ; },
mesh = {*Probiotics ; *Bifidobacterium/physiology/isolation & purification ; *Cultured Milk Products/microbiology ; Fermentation ; Animals ; Food Microbiology ; Humans ; *Dairy Products/microbiology ; },
abstract = {Traditional fermented dairy products (TFDPs) are complex microbial ecosystems that may serve as reservoirs of many microorganisms, including those with probiotic potential such as Bifidobacterium species and lactobacilli. Although bifidobacteria are widely used as probiotic microorganisms in defined formulations, their occurrence, persistence, and functional relevance within TFDPs remain incompletely understood. This review critically synthesizes current evidence on the diversity, ecological roles, and traits associated with probiotic potential of Bifidobacterium spp. detected in TFDPs, including raw-milk fermentations, artisanal dairy products, and selected controlled dairy systems. Species such as Bifidobacterium animalis, Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium breve have been reported across yogurt, kefir, airag (traditional Mongolian fermented dairy beverage from mare milk), and raw milk cheeses, often at low abundance or as transient microbial community members. Many isolates from fermented dairy products exhibit traits commonly associated with probiotic functionality, including acid/bile tolerance, adhesion capacity, exopolysaccharide production, and antimicrobial activity. However, most reports remain limited to presence/absence or in vitro assays, with limited in vivo or clinical validation. Advances in molecular and omics-based approaches have improved detection, characterization, and safety evaluation; however, translation into validated applications remains constrained by challenges in isolation, viability, and strain-level confirmation. Importantly, detection of bifidobacteria in TFDPs does not confer probiotic status, which requires strain-level identification, demonstrated safety, adequate viable counts at consumption, and clinical evidence of health benefit. Collectively, TFDPs, as culturally embedded microbial reservoirs, may support the discovery of novel bifidobacterial strains for future development of functional foods or probiotic products following rigorous validation.},
}

*Probiotics
*Bifidobacterium/physiology/isolation & purification
*Cultured Milk Products/microbiology
Fermentation
Animals
Food Microbiology
Humans
*Dairy Products/microbiology

@article {pmid42333270,
year = {2026},
author = {Ibitoye, OA and Anyanwu, CN and Agbaje, AB and Fasogbon, IV and Dangana, RS and Akinola, SA and Tibyangye, J and Adam, AA and Aja, PM},
title = {Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpag029},
pmid = {42333270},
issn = {2396-8923},
abstract = {Antimicrobial resistance (AMR) is a global health and environmental challenge, driven by complex interactions among microbial communities, resistance genes, and selective pressures in various ecological niches. Traditional surveillance procedures often fall short in capturing the full diversity and dynamics of resistance reservoirs in the environment. This review examines the integration of artificial intelligence (AI) and machine learning (ML) with next-generation sequencing (NGS) technologies for comprehensive resistome profiling. We discuss advances in multi-omics approaches, particularly metagenomics, microbiome-based analytics, and metatranscriptomics. We also highlight computational workflows that enable high-resolution mapping of resistance genes, their mobile genetic elements, and host associations. The role of AI/ML in resistome prediction, classification, and source tracking, as well as the incorporation of environmental metadata for contextual interpretation is discussed based on the selected literature. Moreover, we assess current challenges and propose future directions for developing standardized, scalable, and interpretable bioinformatic pipelines in AMR surveillance. This review primarily elucidates the potential of integrated AI-omics platforms to revolutionize aquatic environmental AMR monitoring and inform risk assessment and mitigation strategies.},
}

@article {pmid42334513,
year = {2026},
author = {Zhang, X and Du, L and Jin, X and Sun, J and An, G and Li, L and Yang, P and Li, F},
title = {Nocardia brasiliensis endophthalmitis initially misdiagnosed as uveitis: a case report.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12348-026-00602-0},
pmid = {42334513},
issn = {1869-5760},
support = {YXKC2020026//Henan Provincial Health Commission/ ; 82301271//National Natural Science Foundation of China/ ; 82230032//National Natural Science Foundation of China/ ; 82101108//National Natural Science Foundation of China/ ; 2025Hx39//First Affiliated Hospital of Zhengzhou University/ ; SBGJ202101011//Health Commission of Henan Province/ ; },
abstract = {BACKGROUND: Endophthalmitis caused by Nocardia brasiliensis is extremely rare and typically affects immunocompromised individuals, frequently leading to severe vision loss due to diagnostic delays. We report a case of N. brasiliensis endophthalmitis in an older man without prior history of systemic immunosuppression but with newly identified diabetes mellitus, characterized by an indolent initial course followed by fulminant progression.

CASE PRESENTATION: A 67-year-old man without known systemic immunosuppression presented with a two-month history of recurrent right-eye pain and redness, followed by rapid vision loss and a hypopyon. Aqueous humor analysis and metagenomic sequencing identified N. brasiliensis. Despite intravitreal amikacin, systemic antimicrobial therapy, and subsequent pars plana vitrectomy with silicone oil tamponade, intraocular inflammation advanced, resulting in worsening corneal opacification, irreversible structural damage, and a final best-corrected visual acuity of light perception.

CONCLUSIONS: N. brasiliensis endophthalmitis may progress rapidly and result in severe, irreversible ocular damage, even in patients without overt systemic immunodeficiency. Early microbiologic identification and prompt, targeted antimicrobial therapy combined with timely surgical intervention are critical, although visual outcomes may remain poor in advanced cases.},
}

@article {pmid42334609,
year = {2026},
author = {Zheng, Y and Chen, C and Guan, D and Huang, Y and Xiong, L and Liu, R},
title = {Viral community dynamics and functional succession in advanced drinking water treatment processes.},
journal = {Archives of microbiology},
volume = {208},
number = {9},
pages = {},
pmid = {42334609},
issn = {1432-072X},
mesh = {*Drinking Water/virology/microbiology ; *Water Purification/methods ; Bacteria/genetics/classification/isolation & purification ; *Viruses/genetics/classification/isolation & purification ; China ; Metagenomics ; Water Microbiology ; },
abstract = {Viruses play a significant role in microbial ecology, yet their impact on drinking water systems remains poorly understood. We collected water from different treatment process streams of an ozone-bioactivated carbon (O3-BAC) advanced drinking water treatment plant in eastern China. DNA viral metagenomic sequencing was then performed to analyze viral abundance, community structure, diversity, host prediction, virulence factors, potential viral pathogens, and functional genes, including carbohydrate-active enzymes (CAZymes), auxiliary metabolic genes (AMGs), and antibiotic resistance genes (ARGs). The results revealed that treatment reduced viral abundance and diversity, although certain taxa not detected in raw water or sedimentation water (e.g., Preplasmiviricota) were detected in sand-filtered water and finished water. Caudoviricetes were the most abundant viruses in the water treatment process. The virus host types were predominantly bacteria, mainly Lactobacillus, Mycoplasma, Staphylococcus, Bacillus, and Streptococcus. Functional analysis revealed viral involvement in carbohydrate degradation via CAZymes and modulation of host metabolism through AMGs and ARGs to support viral replication. Potential human pathogens were identified within Poxviridae and Herpesviridae. This study provides novel insights into DNA viral ecological dynamics in engineered water systems and supports enhanced pathogen control strategies.},
}

*Drinking Water/virology/microbiology
*Water Purification/methods
Bacteria/genetics/classification/isolation & purification
*Viruses/genetics/classification/isolation & purification
China
Metagenomics
Water Microbiology

@article {pmid42334937,
year = {2026},
author = {Ma, C and Liu, S and Won, S and Koslicki, D},
title = {MetagenomicKG: a knowledge graph for metagenomic applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag421},
pmid = {42334937},
issn = {1367-4811},
abstract = {MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored.

RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction.

CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

SUPPLEMENTARY INFORMATION: available at Bioinformatics online.},
}

@article {pmid42334999,
year = {2026},
author = {Masukawa, H and Kobayashi, R and Watanabe, J and Tanizaki, A and Morono, Y and Ito, M and Terada, T and Takaki, Y and Tsuda, M and Matsui, Y and Arai, T and Takai, K and Kameya, M and Arai, H and Yamamoto, M},
title = {Electrosynthetic bacterial growth under conditions simulating electric discharge in deep-sea hydrothermal fields.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag108},
pmid = {42334999},
issn = {1751-7370},
abstract = {Microbial electrosynthesis is a metabolic process in which extracellular electrons are utilized as the primary energy source for carbon fixation. While microbial electrosynthesis has been proposed as a novel concept for ecological primary production, our understanding of how such microorganisms are distributed in natural environments remains limited. In this study, we constructed a laboratory-scale electrochemical cultivation system that simulates electric discharge conditions in deep-sea hydrothermal fields. Microscopic counts revealed increased cell numbers in the electrochemical culture, and 16S rRNA gene analysis revealed a significant enrichment of a novel Thiomicrorhabdus species. Quantitative PCR confirmed proliferation and enrichment of a metagenome-assembled genome (MAG), named the SREC-4. Electrochemical cultivation with 13C-labeled CO2 as a substrate indicated significant 13C incorporation specifically in Thiomicrorhabdus cells including MAG SREC-4. The genome of MAG SREC-4 revealed the possession of the putative extracellular electron uptake pathway in addition to the autotrophic sulfur-oxidizing aerobic respiration pathways typically found in Thiomicrorhabdus members. The putative extracellular electron uptake pathway was found in a phylogenetic clade in Thiomicrorhabdus mainly formed by strains derived from hydrothermal fields. These results provide the direct experimental evidence from enrichment cultures derived from hydrothermal fields that an organism inhabiting deep-sea hydrothermal fields can grow electrosynthetically, and suggest that this ability is shared by other Thiomicrorhabdus species, specifically those found in similar environments. This finding suggests electrosynthetic growth may be widely distributed in Thiomicrorhabdus populations dwelling in deep-sea hydrothermal fields, the largest natural electrogenic environment on Earth.},
}

@article {pmid42335476,
year = {2026},
author = {Valentino, V and De Filippis, F and Ercolini, D},
title = {Fermented foods: lessons learned from metagenomics.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103545},
doi = {10.1016/j.copbio.2026.103545},
pmid = {42335476},
issn = {1879-0429},
abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.},
}

@article {pmid42335503,
year = {2026},
author = {Liu, LM and Fang, HB and Wang, YF and Zhang, YL and Yu, QQ and Zhang, WY and Liu, J and Miao, H and Zhao, YY},
title = {Niaoduqing particles ameliorated tubulointerstitial fibrosis by suppressing IκB/NF-κB signalling pathway via inhibiting host- and gut microbiota-mediated tryptophan co-metabolism.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128592},
doi = {10.1016/j.micres.2026.128592},
pmid = {42335503},
issn = {1618-0623},
abstract = {Tubulointerstitial fibrosis (TIF) is an inevitable outcome of progressive chronic kidney disease (CKD). Niaoduqing particles (NDQ) were developed for the treatment of CKD. However, the molecular mechanisms underlying the effect of NDQ on TIF remain unclear. Fecal gut microbiota (GM) and serum metabolites were analyzed using metagenomics and metabolomics in unilateral ureteral obstruction (UUO)-induced TIF rats. NDQ treatment attenuated UUO-induced TIF in rats in a dose- and time-dependent manner. The increased abundance of eight pathogenic bacteria, including Bacillus wiedmannii, Enterococcus mundtii and Fusobacterium varium, showed strong positive correlations with TID scores, whereas the reduced abundance of two probiotic bacteria, Ruminococcus flavefaciens and Clostridium celatum, showed strong negative correlations with tubulointerstitial damage (TID) scores. NDQ treatment reversed these aberrant microbial alterations, indicating its capacity to remodel GM dysbiosis. TID scores were strongly correlated with host- and GM-mediated tryptophan co-metabolites, including indoxyl sulfate, tryptamine and indole-3-acetic acid, in both TIF- and NDQ-treated TIF rats, and NDQ intervention normalized these metabolic disturbances. Notably, Fusobacterium varium and Enterococcus faecium exhibited strong linear correlations with indoxyl sulfate, indole-3-acetic acid, and indole-3-aldehyde in the TIF rat model. Furthermore, NDQ suppressed IκB/NF-κB signaling pathway in both TIF rats and TGF-β1-induced NRK-52E cells. These inhibitory effects were partially reversed by NF-κB p65 knockdown. This study is the first to demonstrate that NDQ alleviates TIF by reshaping microbial dysbiosis and modulating host- and GM-mediated tryptophan metabolism. These findings support that NDQ mitigates TIF by suppressing IκB/NF-κB signaling pathway through regulation of host-microbiota-derived tryptophan metabolism.},
}

@article {pmid42335537,
year = {2026},
author = {Gong, H and Xian, ZN and Hu, J and Luo, J and Wang, Y and Liu, X and Zhu, N},
title = {Low-intensity electrical stimulation enhances phthalate ester biodegradation by activated sludge through real-time multi-scale regulation.},
journal = {Water research},
volume = {304},
number = {},
pages = {126306},
doi = {10.1016/j.watres.2026.126306},
pmid = {42335537},
issn = {1879-2448},
abstract = {Phthalate esters (PAEs) are ubiquitous contaminants that are poorly removed by conventional biological treatment processes. This study investigated the enhancement of PAE biodegradation in activated sludge under low-intensity electrical stimulation. A single-chamber electrostimulated aerobic microbial system (EAMS) was established and operated at 0.6-2.1 V to explore the physiological, genetic, and community-level responses of microorganisms. Moderate stimulation (0.9-1.5 V, electric field strength 180-300 V·m[-1], current 10.6-136.0 μA, current density 0.5-6.8 mA·m[-2]) increased the biodegradability of the three PAEs by 11%-20%. Electrical stimulation significantly enhanced the physiological activity and community synergy of the microbial community dominated by non-electroactive bacteria. Metagenomic and metatranscriptomic analyses revealed that the genomic abundance of PAE-degrading genes was unchanged, but their expression was strongly upregulated (20-40-fold). Electrical stimulation enhanced PAE biodegradation by activating the metabolic and transcriptional machinery of the resident microbial community, rather than by selecting for specific degraders. This activation led to elevated expression of key degradation genes and consequently improved biodegradation efficiency. These findings suggest that electrical stimulation acts as a functional activator of indigenous microbial communities, providing a rapid and broadly applicable strategy for improving biodegradation efficiency without requiring extensive community restructuring.},
}

@article {pmid42335557,
year = {2026},
author = {Sun, X and Jia, C and Song, X and Zhao, X and Han, M and Yin, H and Zhang, P},
title = {Incorporating benthic microbial thresholds into ecological carrying capacity to sustain ecosystem services of coastal oyster farming.},
journal = {Journal of environmental management},
volume = {413},
number = {},
pages = {130316},
doi = {10.1016/j.jenvman.2026.130316},
pmid = {42335557},
issn = {1095-8630},
abstract = {Oyster aquaculture provides crucial ecosystem services by mitigating coastal eutrophication. However, intensive farming frequently leads to benthic organic overloading, which threatens this bioremediation capacity. Current Ecological Carrying Capacity (ECC) assessments focus on the interaction between yield and pelagic metrics, leaving a critical management loophole regarding benthic sediment health. To address this gap, we conducted a large-scale benthic environmental and metagenomic investigation across five intensive oyster (Crassostrea gigas) farming areas in the Shandong Peninsula, China. Our results revealed that biodeposit-driven organic loading promoted total sulfur (TS) accumulation, triggering a non-linear functional regime shift in the benthic nitrogen cycle. Breakpoint analysis identified a critical threshold at a sedimentary TS concentration of 0.89 g kg[-1], beyond which the denitrification was redirected toward dissimilatory nitrate reduction to ammonium (DNRA), concurrently elevating the risk of greenhouse gas (N2O) emissions. Crucially, a profound spatial decoupling was observed between macroscopic farming yield and benthic micro-ecological status. Shallow-water areas with low yields suffered severe benthic degradation, whereas deep-water areas sustaining highly intensive yields maintained robust eutrophication mitigation functions. This paradox underscores the decisive role of the ecosystem's assimilative capacity over absolute farming load. These findings challenge the traditional yield-focused Ecological Carrying Capacity (ECC) assessments. We therefore advocate for incorporating thresholds of microbial-driven biogeochemical potentials into the ECC management framework to ensure the holistic sustainability of coastal aquaculture.},
}

@article {pmid42335767,
year = {2026},
author = {Li, T and Guo, T and Cui, M and Cao, Y and Zhi, Z and Wang, P and Li, Q and Zhang, J},
title = {Rearing systems shape the successional dynamics of the gut microbiota, resistome, and mobilome in Lueyang Black-boned chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107322},
doi = {10.1016/j.psj.2026.107322},
pmid = {42335767},
issn = {1525-3171},
abstract = {Understanding the ecological factors shaping antimicrobial resistance (AMR) dissemination in agricultural environments is critical for global "One Health". Here, we performed metagenomic sequencing to investigate the impact of intensive cage-reared (CR) and free-range (FR) systems on the gut microbiota, resistome, and mobilome dynamics of Lueyang Black-boned chickens across different production stages. Our analyses revealed that distinct rearing systems drove resistome alterations by reshaping microbial community assembly and horizontal gene transfer (HGT) pathways. Specifically, the CR system imposed strong deterministic stress, thereby enriching opportunistic taxa (such as Desulfovibrio) and promoting a highly connected but topologically fragile microbial network. Conversely, the FR system exhibited a higher total abundance of commensal resistance genes, a process mainly driven by diverse transposon-mediated integrations including tnpA and ISBf10. In contrast, the CR system was associated with high-risk, clinically relevant resistance determinants. These included extended-spectrum beta-lactamases and multidrug resistance cassettes. Targeted network tracking unmasked highly divergent potential host-vector-ARG associations. Resistance expansion under confined CR conditions showed strong vector-dependency, being fundamentally linked to the broad-host-range plasmid IncQ1 alongside clinically relevant mobilization elements, including Class 1 integrons. Longitudinally, the FR resistome achieved ecological stabilization. In contrast, the CR microbiota exhibited continued genetic flux, continuously acquiring transient resistance elements during the observed production period. These findings demonstrate that welfare-friendly rearing management serves as a critical ecological intervention to limit the proliferation of mobile, high-risk resistance traits. Ultimately, future agricultural surveillance must transition beyond quantifying total resistance gene abundance to prioritize functional risk assessments and mobilization potential.},
}

@article {pmid42335821,
year = {2026},
author = {Rehman, A and Wang, X and Yousaf, M and Wang, J and Li, Z},
title = {Biotransformation of Microcystin-LR in marine sediments: Mechanism and global potential.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142754},
doi = {10.1016/j.jhazmat.2026.142754},
pmid = {42335821},
issn = {1873-3336},
abstract = {Microcystin-LR (MC-LR), a potent hepatotoxin produced during cyanobacterial harmful algal blooms, can be transported from freshwater systems to coastal marine environments through riverine discharge and estuarine mixing, yet its environmental fate in coastal sediments remains poorly understood. Here, we investigated the biotransformation mechanism of MC-LR in coastal sediments using LC-MS/MS, metagenomics, metabolic modeling, molecular docking, and genome binning. The results showed that MC-LR was transformed primarily via co-metabolism, following pseudo-first-order kinetics. Notably, we identified a novel biotransformation pathway in the marine environment that differs from the conventionally recognized mlr-dependent pathway observed in terrestrial systems. Biotransformation in marine sediments involves peptide ring opening, formation of linear MC-LR, stepwise peptide shortening, and conversion of the Adda-containing fragment into smaller aromatic compounds. Metabolic modeling and ecological network analysis further revealed that the microbial community facilitates this co-metabolic biotransformation through a cross-feeding mechanism, in which different taxonomic groups share complementary functions for co-substrate transformation, peptide bond cleavage, and aromatic compound degradation. Metagenomic profiling and genome binning demonstrated that MC-LR transformation is coupled with glutathione metabolism, and key genes involved in MC-LR transformation (e.g., CAAX, pepA, pepN, paaA, paaG, paaZ) were mainly associated with members of the Pseudomonadota, Myxococcota, and Acidobacteriota. Global screening of publicly available MAGs revealed that CAAX genes linked to MC-LR transformation are widely distributed across aquatic environments, with 16,209 CAAX-containing MAGs identified from 498 sampling locations worldwide, including 6892 marine MAGs from 317 oceanic sites. Overall, this study clarifies the biotransformation mechanism of MC-LR in marine sediments and highlights the widespread genetic potential for its biotransformation across global aquatic environments.},
}

@article {pmid42335822,
year = {2026},
author = {He, T and Liu, J and Li, Y and Ohgami, N and Wei, X and Peng, T and Zhang, X and Zhang, R and Du, J and Deng, Y and Jiang, H and Zhang, P and Zhang, Y},
title = {Long-term groundwater arsenic exposure is associated with altered arsenic methylation capacity and gut microbiota composition in a rural Chinese population.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142658},
doi = {10.1016/j.jhazmat.2026.142658},
pmid = {42335822},
issn = {1873-3336},
abstract = {This study investigated the relationship between long-term groundwater arsenic exposure, arsenic methylation capacity, and gut microbiota in adults from rural northern China. Arsenic detoxification relies in part on methylation processes, and growing evidence suggests that the gut microbiome may participate in arsenic biotransformation, yet population-based data integrating exposure, metabolism, and microbial profiles remain scarce. We recruited 258 participants from two neighboring villages supplied by centralized wells with contrasting arsenic levels (control, n = 138; exposure, n = 120). Total urinary arsenic was measured in all participants, and arsenic species were quantified in a subgroup (n = 60) to derive primary and secondary methylation indices (PMI and SMI). Fecal metagenomes were sequenced to characterize taxonomic composition and functional potential based on KEGG and GO annotations. Individuals in the exposure village showed higher levels of urinary inorganic arsenic and methylated metabolites. While PMI was comparable between groups, SMI was significantly reduced among exposed individuals, indicating impaired secondary methylation. Arsenic exposure was also associated with pronounced alterations in gut microbial diversity and community structure. Several anaerobic taxa, largely linked to fermentative metabolism, were positively associated with SMI after multivariable adjustment. Functional analyses further revealed differences in pathways related to transport, environmental sensing, and metabolism. These findings suggest that chronic arsenic exposure is associated with reduced methylation efficiency and shifts in gut microbial composition and function, and that the gut microbiome may contribute to interindividual variability in arsenic metabolism and toxicity.},
}

@article {pmid42335936,
year = {2026},
author = {Ter Horst, PAG and Marshall, IPG and Egas, RA and Klomp, R and Schutgens, MAW and van Alen, T and Jetten, MSM and Slomp, CP and Welte, CU},
title = {Electrogenic CH4 oxidation on a bioanode: putative extracellular electron transport system in Methylobacter sp.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag067},
pmid = {42335936},
issn = {1574-6941},
abstract = {Aerobic methanotrophs are frequently detected in oxygen-limited, stratified coastal environments. Known adaptations, including high-affinity terminal oxidases and oxygen-binding bacteriohemerythrins, help explain methane oxidation at extremely low oxygen concentrations, yet their activity and ecological role under fully anoxic conditions remain uncertain. Here, we show that an anoxic, poised-anode bioelectrochemical system inoculated with a methane-oxidizing sediment enrichment produced methane-dependent current, with rapid current loss upon methane removal and recovery after re-addition. Metagenomic analysis revealed the selective enrichment of a Methylobacter population encoding a porin-cytochrome complex and numerous multiheme c-type cytochromes, suggesting extracellular electron transfer potential. A complementary phylogenomic survey across Methylococcales identified homologs of this gene cluster in multiple lineages, but with a scattered phylogenetic distribution indicative of modular acquisition. Comparative synteny further revealed conserved gene order across genomes, supporting horizontal transfer of the locus as a functional unit. Together, these results demonstrate that aerobic methanotrophs may employ extracellular electron transfer strategies to dissipate methane-derived electrons when oxygen-dependent respiration is constrained.},
}

@article {pmid42336533,
year = {2026},
author = {Yu, L and Jiang, L and Liu, C and Wang, S and Zhu, G},
title = {High co-occurrence but low heterogeneity of virulence factors and resistance genes in farmland soil.},
journal = {Journal of environmental sciences (China)},
volume = {166},
number = {},
pages = {273-282},
doi = {10.1016/j.jes.2025.11.031},
pmid = {42336533},
issn = {1001-0742},
abstract = {Virulence factors (VFs), antibiotic resistance genes, and metal resistance genes in farmland soil pose significant threats to food security, soil health, and human well-being. Numerous studies have reported on the characteristics and hazards of resistance genes in the soil, but the co-occurrence of VFs and resistance genes has received little attention as a potential threat to the ecological environment. Here, we investigated the mechanism of interaction between VFs and resistance genes in farmland soil samples worldwide, especially in China, the most antibiotic-contaminated country. Metagenomics and metagenome binning analysis provided direct evidence that VFs and resistance genes could co-occur universally in the same microbial cell in farmland soil, dramatically enhancing the pathogenic ability of soil microorganisms and severely raising the threat to ecological security. We found that the spatial distribution of resistance genes and VFs in farmland topsoil exhibited low heterogeneity. These findings contribute to our understanding of VFs and resistance genes in farmland soil, which is beneficial for ensuring the healthy development of agriculture and food security.},
}

@article {pmid42336534,
year = {2026},
author = {Zhai, F and Li, B and Zhao, X and Zhao, P and Yang, S and Li, X and Wang, T and Liu, G and Yan, P},
title = {Bioelectrochemical mitigation of soil antibiotic resistance: Disruption of bacteriophage transmission and resistant hosts.},
journal = {Journal of environmental sciences (China)},
volume = {166},
number = {},
pages = {283-294},
doi = {10.1016/j.jes.2025.11.008},
pmid = {42336534},
issn = {1001-0742},
abstract = {The proliferation of antibiotic resistance genes (ARGs) in environment poses a threat to global public health. Although microbial fuel cell (MFC) has been demonstrated to mitigate ARG amplification, the mechanism remains unclear. This study employed metagenomic sequencing combined with the DeepARG-LS model for profiling ARGs and further analyzed the effects of MFCs on them in tetracycline-contaminated soil. Consequently, tetracycline addition (AT treatment) elevated total ARG abundance by 31 %, whereas MFC application (MT treatment) reduced it by 12 %. The deep learning model revealed a 38 % reduction in the richness of ARG subtypes in the MT compared to the AT. Proteobacteria dominated as ARG hosts, accounting for 78 % of ARGs in the AT, but declined by 18 % in the MT. Notably, the archaeal Nitrososphaeraceae was identified as a host for tetA(48). Species-level analysis identified 12 ARG-carrying bacterial taxa, the abundance of most of which was suppressed (abundance) by MFCs. The richness of ARGs host bacteria was 38 % lower in the MT treatment than that in the AT treatment. Meanwhile, the abundance of the indole biosynthesis gene (tryptophanase, EC 4.1.99.1) exhibited a consistent trend with the richness of ARGs hosts. Mechanistically, the suppression of ARG-host bacteria may be attributed to enhanced indole biosynthesis (as indicated by increased tryptophanase abundance), coupled with reduced abundances of mobile genetic elements (84 %) and virulence factors (11 %), and a decline in phage-mediated ARG transmission (19 %). Overall, these findings provide insights into bioelectrochemical controlling ARG dissemination in soils.},
}