@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41915167},
issn = {1432-184X},
abstract = {UNLABELLED: Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02730-5.},
}

@article {pmid41917256,
year = {2026},
author = {Shen, Z and Liu, Y and Liu, Y and Zhang, P and Li, Y and Li, Z and Qi, H},
title = {Clinical characteristics and mixed infection patterns of ocular surface infection with Epstein-Barr virus.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {16},
number = {1},
pages = {},
pmid = {41917256},
issn = {1869-5760},
abstract = {PURPOSE: To analyze the clinical features of ocular surface diseases caused by Epstein-Barr virus (EBV) infection.

METHODS: A retrospective case series study was conducted. Data from 48 patients (54 eyes) with EBV infection who visited Peking University Third Hospital between January 2023 and October 2025 were collected. Patient demographics and baseline information were recorded. Ophthalmic slit-lamp examination, ocular surface (conjunctiva/cornea) scrapings, bacterial culture of ocular secretions, real-time fluorescence quantitative PCR detection, EBV-specific antibody testing, and metagenomic next-generation sequencing (mNGS) were performed.

RESULTS: Among patients infected with EBV on the ocular surface, the majority were middle-aged individuals in the 31–40 age group. The primary risk factors for onset were keeping pets (10/48), followed by colds (6/48); among those keeping pets, parrots were the most common (5/9). The main clinical manifestations were foreign body sensation (37/54) and yellow discharge (34/54). Common signs included mixed conjunctival hyperemia (31/54), follicles on the lower eyelid conjunctiva (17/54), papillae on the upper eyelid conjunctiva (8/54), and punctate epithelial defects on the cornea (17/54). In most ocular surface scrapings, small round lymphocytes were observed alongside a small number of reactive lymphocytes (44/54), which could simultaneously present with a large number of neutrophils (36/54). There was a significant difference between the presence of yellow discharge and the type of conjunctival hyperemia [Formula: see text]. However, no statistically significant correlation was found between the presence of yellow discharge and the presence of neutrophils in the scraping results [Formula: see text]. Significant differences were found in EBV viral loads among different groups of combined symptoms [Formula: see text] and among different follicle groups [Formula: see text]. No statistically significant correlation was found between the lymphocyte count in the scraping and the EBV viral load in the affected eye [Formula: see text].

CONCLUSION: EBV infection of the ocular surface is prone to concurrent infections; therefore, a detailed medical history inquiry is crucial. Ocular surface tissue scraping examination can rapidly identify viral infection-related inflammatory characteristics and rule out bacterial/fungal infections, providing effective supportive auxiliary diagnostic evidence for viral ocular surface infection, and precise diagnosis of EBV infection needs to be achieved in combination with molecular biological and serological tests.},
}

@article {pmid42014454,
year = {2026},
author = {Muller, E and Bamberger, T and Borenstein, E},
title = {Navigating multi-omic integration methods for human microbiome research.},
journal = {Nature microbiology},
volume = {11},
number = {5},
pages = {1153-1167},
pmid = {42014454},
issn = {2058-5276},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2266/25//Israel Science Foundation (ISF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Host Microbial Interactions ; *Metagenomics/methods ; Multiomics ; },
abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
Host Microbial Interactions
*Metagenomics/methods
Multiomics

@article {pmid42128850,
year = {2026},
author = {Fujii, N and Nakajima, M and Narihiro, T and Kuroda, K and Kindaichi, T},
title = {Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25084},
pmid = {42128850},
issn = {1347-4405},
mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Phylogeny ; Ecosystem ; Genome, Bacterial ; },
abstract = {The phylum Minisyncoccota (formerly known as "Candidatus Patescibacteria"/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.},
}

*Bacteria/classification/genetics/isolation & purification/metabolism
Phylogeny
Ecosystem
Genome, Bacterial

@article {pmid42129189,
year = {2026},
author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E},
title = {Network topology of the gut microbiome associates with metabolic health in obesity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42129189},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; },
abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Male
Female
*Obesity/microbiology/metabolism
Middle Aged
Cross-Sectional Studies
Adult
Feces/microbiology
Metagenomics
*Obesity, Metabolically Benign/microbiology/metabolism
Dysbiosis/microbiology
Phenotype

@article {pmid42129350,
year = {2026},
author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D},
title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01626-2},
pmid = {42129350},
issn = {2730-664X},
abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.

OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.

DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.

RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p = 0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.

CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.

TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.},
}

@article {pmid42129659,
year = {2026},
author = {Chen, J and Li, X and Deng, Z and Ying, Y and Lu, M},
title = {Clinical characteristics of sporadic acute Q fever diagnosed by metagenomic next-generation sequencing: a retrospective analysis and literature review in China.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13477-2},
pmid = {42129659},
issn = {1471-2334},
support = {MISP-102684//MSD Investigator Initiated Studies Program Review Committee/ ; 2022YFC2303203-01//National Key Research and Development Program of China/ ; Z-2017-24-2202//Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; },
abstract = {BACKGROUND: Acute Q fever manifests sporadically in mainland China, where its clinical spectrum and optimal diagnostic strategies remain under-recognized. This study aimed to delineate the clinical phenotype and antimicrobial prescribing patterns of sporadic acute Q fever diagnosed via metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective, single-center cohort study of adult patients with sporadic acute Q fever. A comprehensive literature review of all published sporadic cases across China was subsequently performed to delineate the national clinical spectrum of sporadic Q fever.

RESULTS: The cohort comprised 22 male patients (mean age 36.7±13.5 years). All patients presented with high-grade pyrexia (>39°C) accompanied by a characteristic symptom constellation of headache, fatigue, myalgia, and hepatic involvement (100%, mean ALT 122.2±56.9 U/L). Pneumonia was observed in 2 patients (2/22, 9.1%). A distinct dissociation was observed between markedly elevated C-reactive protein (mean 67.4 ± 33.6 mg/L) and normal leukocyte counts. A pooled analysis of 94 published cases and 22 consecutive patients from our center yielded 116 confirmed Q fever cases (male-to-female ratio 11.9:1, the proportion of hepatitis and pneumonia:87.9% and 24.1%) The median interval from symptom onset to pathogen confirmation was 7.8 ± 2.8 days. mNGS yielded a diagnosis in 77.5 % of 116 patients, the remaining 22.5 % were identified by PCR and antibody testing.

CONCLUSION: Acute Q fever in China predominantly affects young males, presenting as a systemic febrile illness with a distinctive hepatic phenotype (elevated liver enzymes) rather than prominent pneumonia. The clinical triad of high fever, influenza-like symptoms (headache/myalgia), and "WBC-CRP dissociation" (normal white cell count with elevated CRP) serves as a potential clinical indicator. Empiric doxycycline should be initiated promptly in suspected cases. mNGS is a valuable tool for definitive diagnosis, particularly when empiric therapy fails or in severe/complicated cases.},
}

@article {pmid42129710,
year = {2026},
author = {Wang, Z and Tang, J and Yang, K and Cui, Z and Li, Z},
title = {Diagnostic challenges and lessons learned of Guillain-Barré syndrome mimicking central nervous system infection - a case report.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04942-1},
pmid = {42129710},
issn = {1471-2377},
abstract = {BACKGROUND: Guillain-Barré syndrome (GBS) is an immune-mediated disorder affecting the peripheral nervous system, often triggered by infections, vaccinations, trauma, or surgery. Typically, it presents as progressive, symmetric limb weakness with hyporeflexia. However, some GBS subtypes can present atypically with symptoms like headache, facial palsy, and confusion. These symptoms overlap significantly with central nervous system (CNS) infections, often causing diagnostic delays.

CASE PRESENTATION: A 57-year-old man was admitted with cough, sputum, and shortness of breath, having received a rabies vaccination a month earlier. He developed headache, dysphagia, progressive muscle weakness, and impaired consciousness, requiring Intensive Care Unit (ICU) transfer, endotracheal intubation, and mechanical ventilation. The initial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa (sequence count: 6094), combined with fever and a series of clinical symptoms before transfer to the ICU, CNS infection was considered. Treatment with piperacillin-tazobactam, meropenem, and ciprofloxacin yielded no improvement. Albumino-cytological dissociation in the CSF led to a neurology consultation for suspected GBS, and intravenous immunoglobulin (IVIg) therapy began. Negative CSF bacterial cultures and mNGS, along with positive anti-GT1a IgM ganglioside antibodies and electromyogram(EMG) result indicating nerve damage, confirmed the GBS diagnosis. After five days of IVIg, the patient was weaned from mechanical ventilation and showed significant neurological recovery.

CONCLUSION: The significant clinical overlap between GBS and CNS infections poses a major diagnostic and therapeutic challenge. This case highlights the importance of thorough history-taking, comprehensive neurological assessment, careful interpretation of lab results, and early neurologist involvement to minimize diagnostic delays in GBS and prevent subsequent treatment delays.},
}

@article {pmid42129938,
year = {2026},
author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z},
title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02426-5},
pmid = {42129938},
issn = {2049-2618},
support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.},
}

@article {pmid42130304,
year = {2026},
author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z},
title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70324},
pmid = {42130304},
issn = {1462-2920},
support = {LP160101508//Australian Research Council/ ; },
mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Islands ; Coral Reefs ; },
abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.},
}

*Anthozoa/microbiology/growth & development
Animals
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota
*Seawater/microbiology
Islands
Coral Reefs

@article {pmid42130363,
year = {2026},
author = {DU, WQ and Liu, LJ and Zhang, L and Tang, YF and Liu, LQ and Li, XF and Xiao, YY},
title = {[A case of Bartonella henselae meningitis characterized by bone marrow hemophagocytosis].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {28},
number = {5},
pages = {618-623},
pmid = {42130363},
issn = {1008-8830},
mesh = {Humans ; Male ; Adolescent ; *Bartonella henselae ; *Cat-Scratch Disease/complications ; *Lymphohistiocytosis, Hemophagocytic/etiology ; *Bone Marrow/pathology ; *Meningitis, Bacterial ; },
abstract = {A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.},
}

Humans
Male
Adolescent
*Bartonella henselae
*Cat-Scratch Disease/complications
*Lymphohistiocytosis, Hemophagocytic/etiology
*Bone Marrow/pathology
*Meningitis, Bacterial

@article {pmid42130962,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {7},
number = {1},
pages = {9-20},
pmid = {42130962},
issn = {2641-6549},
abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.

MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.

RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).

CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.},
}

@article {pmid42131203,
year = {2026},
author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A},
title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758563},
pmid = {42131203},
issn = {1664-302X},
abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.

METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.

RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.

DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.},
}

@article {pmid42131208,
year = {2026},
author = {Hembram, DB and Panda, SP and Das, BK and Soren, D and Singh, NR},
title = {Microbial elicitors to metabolic reprogramming: an integrative model of plant-microbe interactions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1816468},
pmid = {42131208},
issn = {1664-302X},
abstract = {Plant growth, soil health, and crop productivity with nutritional quality can be significantly enhanced by employing microbial consortia that incorporate diverse microorganisms with complementary functions. Plants produce various types of secondary metabolites such as terpenoids, alkaloids, phenolics, essential oils, and other metabolites through various cellular mechanisms, which are often stimulated by microbial interactions. These metabolites exert beneficial effects on plants and perform multiple roles in agriculture, contributing significantly to growth and economy. This review summarizes microbial consortia-mediated enhancement of plant health and their intricate interactions with host plants. Beneficial microbes of a consortium trigger complex signaling cascades leading to a dynamic regulatory strategy through which plants enhance their secondary metabolite synthesis. Secondary messengers and hormonal cross-talk further integrate the signal to transcription factors, which play a central role in activating or repressing the key genes of the metabolic pathways. Thus, the interplay of microbial signal, secondary messengers, hormonal cross-talk, and key metabolite genes forms the basis of plant secondary metabolite biosynthesis. In addition, recent advances in systems microbiology, including metagenomics, metatranscriptomics, and metabolomics, have enabled a holistic understanding of microbial community dynamics and their collective role in regulating secondary metabolism.},
}

@article {pmid42131214,
year = {2026},
author = {Sudianto, E and Shlafstein, MD and Durieu, B and Harmel, M and Cornet, L and Saw, JH},
title = {Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824103},
pmid = {42131214},
issn = {1664-302X},
abstract = {INTRODUCTION: Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy.

METHODS: Analysis of 46 steam vent associated samples from Hawai'i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes.

RESULTS: This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material.

CONCLUSION: These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.},
}

@article {pmid42131265,
year = {2026},
author = {Cheng, J and Ni, J and Zhao, Y and Jiang, L and Huang, Y and Zhang, Y and Yan, P and Long, Z and Fu, H and Jiang, X},
title = {The clinical utility of metagenomic next-generation sequencing in the management of fever in patients with hematological disorders.},
journal = {Nagoya journal of medical science},
volume = {88},
number = {1},
pages = {84-98},
pmid = {42131265},
issn = {2186-3326},
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Adult ; *Metagenomics/methods ; Aged ; *Hematologic Neoplasms/complications/microbiology ; *Fever/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Patients with hematological malignancies frequently present with severe and intricate infections that pose life-threatening risks. Conventional pathogen detection methods offer limited clinical insights and therapeutic guidance. This retrospective study evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in hematologic patients who remained febrile despite prolonged antibiotic therapy, which means unresponsive to antibiotic therapy. This retrospective analysis included 204 patients with hematologic malignancies, undergoing conventional pathogen detection and peripheral blood mNGS. The cohort was stratified into neutropenia and non-neutropenia groups to compare the diagnostic and therapeutic implications of mNGS versus conventional microbiological tests (CMT). Among the 204 patients with mNGS, the overall positive detection rate was significantly higher than that of CMT (68.1% vs 30.9%, P<0.001). In both the neutropenia and non-neutropenia group, mNGS demonstrated a higher positivity rate for bacteria than for CMT (bacteria, 36.4% vs 15.6%, P<0.01). mNGS proved notably advantageous for bloodstream infections with clinically relevant drug-resistant strains, particularly in the neutropenia cohort (26.4% vs 12.5%, P<0.001). Using a composite reference standard, mNGS manifested sensitivity and specificity rates of 78.4% and 61.9%, respectively. Patients in the neutropenia group derived superior clinical benefit from mNGS, including higher diagnostic accuracy and treatment efficacy (diagnosis, 56.4% vs 40.6%, P=0.036; treatment, 49.3% vs 31.3%, P = 0.016). Additionally, the 30-days mortality rate was notably higher among mNGS-positive patients who tested compared to those who tested negative (17.3% vs 1.5%, P<0.001). mNGS demonstrated clinical relevance in patients with hematologic malignancy who received prolonged antibiotic treatment and holds promise in predicting patient survival prognosis.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Adult
*Metagenomics/methods
Aged
*Hematologic Neoplasms/complications/microbiology
*Fever/microbiology/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use

@article {pmid42131305,
year = {2026},
author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F},
title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1769892},
pmid = {42131305},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; },
abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.

METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.

RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.

DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.},
}

Humans
*Colitis, Ulcerative/microbiology/immunology
*Mycobiome
*Gastrointestinal Microbiome
Adult
Child
Male
Female
*Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Middle Aged
Young Adult
Adolescent
Dysbiosis/microbiology
Metagenome
Child, Preschool
Age Factors
Aged
Feces/microbiology

@article {pmid42131468,
year = {2026},
author = {Mazibuko, X and Mtimka, S and Ngobese, LM and Mafuna, T and Simelane, MB and Yakobi, SH and Gumede, X and Pooe, OJ},
title = {Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation.},
journal = {Bioinformatics and biology insights},
volume = {20},
number = {},
pages = {11779322251413418},
pmid = {42131468},
issn = {1177-9322},
abstract = {Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria, Acidobacteria, and Bacteroidetes, and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity's role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.},
}

@article {pmid42131611,
year = {2026},
author = {Zhai, X and Pan, H and Zheng, J},
title = {Spinal infection caused by Coxiella burnetii and surgical treatments: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1785109},
pmid = {42131611},
issn = {2296-858X},
abstract = {Q fever is a rare global zoonosis caused by Coxiella burnetii, with bone and joint involvement being an uncommon manifestation that poses significant diagnostic challenges. This article reports a case of persistent focal spinal infection caused by C. burnetii in an elderly female without a clear epidemiological exposure history, who was initially misdiagnosed with vertebral compression fractures. The diagnosis was confirmed by third-generation nanopore-based metagenomic next-generation sequencing (mNGS), which detected 12,170 reads of C. burnetii with a relative abundance of 98.27%. The patient was initially treated with oral doxycycline (0.1 g q12h) and rifampin capsules (0.45 g daily) for 4 weeks, resulting in decreased inflammatory markers and reduced paravertebral abscess size. After clinical stabilization, surgical intervention (posterior approach T12-L1 vertebral lesion resection, intervertebral bone graft fusion, and pedicle screw rod fixation) was performed under general anaesthesia. Postoperative follow-up for 3 months showed a significant improvement in the patient's low back pain [visual analogue scale (VAS) score from 6 preoperatively to 1 at 3 months] and functional status [Oswestry Disability Index (ODI) from 65% preoperatively to 10% at 3 months], with normalized inflammatory markers and a reduced C. burnetii IgG antibody titre (from 1:256 to 1:128). Serological follow-up revealed persistent negative IgM antibodies throughout the treatment course. This case highlights the diagnostic value of third-generation mNGS for rare spinal infections caused by C. burnetii and the efficacy of a multimodal treatment approach combining targeted antimicrobial therapy and surgical intervention. The rationale for antibiotic selection and surgical management is discussed, along with the limitations of the present case and clinical insights for managing similar cases.},
}

@article {pmid42132311,
year = {2026},
author = {Tulloch, RL and Rojahn, J and Neaves, LE and Trujillo-González, A and Holleley, CE and Hahn, EE},
title = {Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70153},
doi = {10.1111/1755-0998.70153},
pmid = {42132311},
issn = {1755-0998},
support = {//Centre for Biodiversity Analysis/ ; },
mesh = {*DNA/isolation & purification/genetics ; *Specimen Handling/methods ; Animals ; Metagenomics/methods ; DNA Barcoding, Taxonomic/methods ; Museums ; *Preservation, Biological/methods ; },
abstract = {Advancements in historical genomics increasingly leverage museum collections to study past ecosystems, species interactions and biodiversity. Formalin-fixed, ethanol-preserved specimens, once thought inaccessible to molecular analyses due to DNA degradation, are emerging as valuable genomic resources. If recoverable and reliably attributable, DNA within preservation media could provide a non-destructive alternative to conventional tissue sampling, with the potential to expand molecular access to valuable or irreplaceable specimens. We tested whether preservation media contains recoverable DNA suitable for taxonomic inference. We coupled passive adsorption and active filtration of specimen media with hot alkaline lysis DNA extraction followed by metabarcoding and shotgun metagenomics. DNA was recoverable across samples, including 41 of 61 (~67%) targets in a composite sample. However, detections were dominated by non-target taxa, indicating that preservation media retain a layered mixture of specimen-derived DNA and broader collection-level background. Detection success tracked with preservation chemistry (near-neutral pH and low residual formaldehyde) rather than specimen age. Method choice influenced detections: active filtration increased target detections but admitted more background; passive capture was sparser but more selective; shotgun sequencing retrieved broader vertebrate signals, including reptiles, but was heavily enriched for non-targets. Because both target and non-target taxa were often abundant, read-abundance cut-offs were unreliable for attribution. Spirit-media DNA is therefore best interpreted as a collection-level signal and a screening tool to identify jars with molecular potential (e.g., taxa of conservation or biosecurity interest), rather than as a definitive non-destructive proxy for specimen identity. Prioritising chemically favourable jars and implementing rigorous contamination controls should improve signal interpretability and help unlock the value of preservation media for historical genomics.},
}

*DNA/isolation & purification/genetics
*Specimen Handling/methods
Animals
Metagenomics/methods
DNA Barcoding, Taxonomic/methods
Museums
*Preservation, Biological/methods

@article {pmid42132424,
year = {2026},
author = {Bae, J and Takemura, M},
title = {Refining a giant virus lineage: a novel order unifying Mamonoviridae and "Manesviridae," unveiled by the discovery of furtivovirus.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0203125},
doi = {10.1128/jvi.02031-25},
pmid = {42132424},
issn = {1098-5514},
abstract = {UNLABELLED: The evolutionary origins and taxonomic framework of giant viruses related to the family Mamonoviridae and its relative group, including clandestinovirus, remain unclassified due to gaps in genome size and host range between these two groups. This study aimed to address this gap by integrating our newly isolated virus with publicly available metagenome-assembled genomes (MAGs) to construct a more robust phylogenetic framework. Here, we report the isolation and characterization of a new giant virus, furtivovirus, using the unicellular amoeba Vermamoeba vermiformis as a host. Furtivovirus has a genome of approximately 560 kbp and shares key features with its closest relative, clandestinovirus. Ultrastructural analysis revealed a unique host-nucleus-dependent replication strategy characterized by the breakdown of the nuclear membrane and the packaging of nascent virions directly within the nucleoplasm, distinguishing it from canonical cytoplasmic virion factories. Comprehensive phylogenetic and comparative genomic analyses of shared orthologous groups and nucleocytovirus marker proteins revealed that furtivovirus, clandestinovirus, ushikuvirus, and usurpativirus form a distinct monophyletic clade, for which we propose a new family, "Manesviridae." Further analysis using amino acid-based similarity metrics of Nucleocytoviricota viral genomes, including established MAGs, demonstrated that this new family is robustly placed as a sister group to the family Mamonoviridae. This study elucidated the evolutionary relationships between viruses with large and small genomes that possess similar virion sizes within this lineage. Based on this cumulative evidence, we propose the establishment of a new order to unify these two families, thereby expanding their diversity and clarifying the evolutionary history of this branch within Nucleocytoviricota.

IMPORTANCE: Giant viruses challenge our traditional understanding of viral evolution, raising the question of how a single related group can diverge to infect different hosts while evolving into vastly different genome sizes and replication strategies. The family Mamonoviridae and its relatives epitomize this evolutionary divergence: one group possesses massive genomes, whereas the other has genomes that are less than half their size. The discovery of furtivovirus and its unique nucleoplasm-dependent replication cycle provides a critical biological context for this genomic disparity. Through deep comparative genomic analysis, we demonstrated that these seemingly disparate lineages share a cohesive evolutionary origin that is distinct from other established orders. This finding highlights the complexity of genome evolution, demonstrating that giant viruses can expand their overall genome size to adapt to uncertain environments while reducing their core essential genes, thereby providing new insights into the evolutionary pressures that shape the diversity of the virosphere.},
}

@article {pmid42132850,
year = {2026},
author = {Bright, K and Dienes, B and van Dongen, B and Strashnov, I and Han, X and Aeppli, M},
title = {Emerging investigator series: metagenomic insights into microbial controls of carbon cycling in alpine soils.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5em01047k},
pmid = {42132850},
issn = {2050-7895},
abstract = {Alpine riparian zones span topographic gradients from wet soils on the plain near streams to drier soils on adjacent slopes. These differences in soil moisture are generally associated with shifts in the soil redox state from anoxic on the plain to oxic on the slope. In anoxic plain soils, soil organic carbon (SOC) may accumulate due to thermodynamic constraints on microbial activity. Here, we used shotgun metagenomics to examine how microbial diversity and functional potential vary across differing redox conditions on plain and slope soils in two catchments in the Swiss Alps. We complemented these analyses with soil physicochemical characteristics and information on the chemical composition of organic matter. Plain soils had higher SOC stocks and higher relative abundance of phenol compounds relative to slope soils, consistent with SOC preservation and preferential mineralisation of easily degradable organic compounds under anoxic conditions. Microbial communities in plain soils further exhibited greater taxonomic and functional diversity, including increased potential for anaerobic respiration pathways. Genes for nitrate, iron, and sulfate reduction were linked to the Chloroflexota, Acidobacteria, and Desulfobacterota phyla, respectively. Based on NMDS correlations, electron accepting capacity, calcium content, and pH shaped microbial community composition. Slope soils, by contrast, supported less diverse microbial communities, determined mainly by electron donating capacity and clay content. Our work demonstrates how soil redox conditions and microbial functional potential shape carbon cycling across landscape positions in alpine riparian zones. This mechanistic understanding is critical to anticipate changes in carbon cycling in alpine ecosystems in a changing climate.},
}

@article {pmid42132937,
year = {2026},
author = {Enuh, BM and Myers, KS and Bott, C and Klaus, S and McCullough, K and McIntosh, L and Beach, N and Young, M and Donohue, TJ and Noguera, DR},
title = {Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0149225},
doi = {10.1128/mra.01492-25},
pmid = {42132937},
issn = {2576-098X},
abstract = {Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.},
}

@article {pmid42132952,
year = {2026},
author = {Özel, Ş and Lauritano, D},
title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42132952},
issn = {1573-4978},
mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Mouth Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dysbiosis/microbiology ; Case-Control Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; Recurrence ; },
abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.},
}

Humans
*Stomatitis, Aphthous/microbiology/genetics
*Mouth Mucosa/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Dysbiosis/microbiology
Case-Control Studies
Saliva/microbiology
Bacteria/genetics/classification
Recurrence

@article {pmid42133155,
year = {2026},
author = {Zhang, Q and He, G and Guo, Z and He, Y and Xiong, J and He, T and Lee, SL},
title = {Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils and a forest-derived fermentation-enriched microbial community.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42133155},
issn = {1573-0972},
support = {42367039, 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//National Key Research and Development Program of China/ ; Z2024417//Guizhou Provincial Science and Technology Department/ ; Liu Jin Xiang [2024] No. 44, 202406670023//Overseas Study Program for Young Key Teachers/ ; },
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Zea mays/growth & development/microbiology ; Forests ; Fermentation ; Soil/chemistry ; *Metagenomics/methods ; *Fertilizers ; *Metabolomics/methods ; China ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Agriculture ; Carbon/metabolism ; },
abstract = {Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.},
}

*Nitrogen/metabolism
*Soil Microbiology
*Zea mays/growth & development/microbiology
Forests
Fermentation
Soil/chemistry
*Metagenomics/methods
*Fertilizers
*Metabolomics/methods
China
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Agriculture
Carbon/metabolism

@article {pmid42133463,
year = {2026},
author = {Che, J and Du, J and Piao, Y and Dong, Y and Zhang, L and Su, D and Zhang, C and Zhao, Y and Du, W and Che, N},
title = {Fungal Species Identification in FFPE Tissues: A Comparative Evaluation of Droplet Digital PCR, ITS Sequencing, and Metagenomic Next-Generation Sequencing.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag049},
pmid = {42133463},
issn = {1460-2709},
abstract = {Accurate histological diagnosis of fungal infections is challenging due to morphological similarities among fungi, which can affect treatment outcomes. This study evaluated the performance of droplet digital PCR (ddPCR), internal transcribed spacer (ITS) sequencing, and metagenomic next-generation sequencing (mNGS) using 111 formalin-fixed, paraffin-embedded tissue samples with histologically confirmed fungal infections. All three methods showed comparable detection rates for filamentous fungi (84.2%-94.7%; p = 0.2). For yeast-like fungi, however, mNGS demonstrated significantly higher detection (66.7%) than ddPCR (46.3%) and ITS sequencing (35.2%) (p < 0.01). mNGS also achieved superior genus- and species-level identification (81.1% for both) compared to ddPCR (65.8% and 64.9%) and ITS sequencing (61.3% and 50.5%) (p < 0.01). Additionally, mNGS identified two unusual fungi (Scedosporium apiospermum and Schizophyllum commune) previously misdiagnosed as Aspergillus. These findings support the integration of mNGS into clinical diagnostic workflows for the accurate identification of yeast-like and rare fungal pathogens, thereby enabling targeted antifungal therapy.},
}

@article {pmid42133477,
year = {2026},
author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW},
title = {Gut Species Porphyromonas asaccharolytica and Bacteroides fragilis Are Associated with Whole Body Fat Percentage.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag117},
pmid = {42133477},
issn = {1365-2672},
abstract = {AIMS: Obesity is linked to various adverse health effects, with body fat percentage being a key indicator of these risks. While the gut microbiota (GM) plays important roles in obesity, the specific species involved remain poorly understood. We aimed to identify gut species that may influence obesity in a cohort of US men.

METHODS AND RESULTS: We conducted a comprehensive integrative analysis using metagenomics and whole-genome sequencing data in the US cohort. MaAsLin2 was used to identify associations between GM and whole body fat percentage (PFAT). Mendelian randomization (MR) was applied to investigate potential directional relationships between GM species and PFAT, as well as possible interactions between microbial species. Porphyromonas asaccharolytica (P.asaccharolytica) was negatively associated (β=-0.181, P=0.005) with PFAT, while Bacteroides fragilis (B.fragilis) was positively associated (β=0.239, P=0.001); these associations were validated in an independent Chinese cohort. MR analysis suggested that P.asaccharolytica may influence PFAT in part through its potential effect on B. fragilis abundance.

CONCLUSION: Gut species P.asaccharolytica and B.fragilis are associated with host body fat percentage and may influence obesity individually or collaboratively. The observed associations provide evidence consistent with a potential directional relationship between these species and human adiposity.},
}

@article {pmid42133579,
year = {2026},
author = {Lai, X and Gao, Q and Wu, L},
title = {A 56-Year-Old Male Farmer From China With Severe Fever With Thrombocytopenia Syndrome and Pulmonary Aspergillosis: A Case Report and Review of Literature.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e951798},
doi = {10.12659/AJCR.951798},
pmid = {42133579},
issn = {1941-5923},
mesh = {Humans ; Male ; Middle Aged ; *Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications ; China ; *Pulmonary Aspergillosis/diagnosis/complications ; Farmers ; COVID-19 ; Coinfection ; Aspergillus fumigatus/isolation & purification ; Antifungal Agents/therapeutic use ; },
abstract = {BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease caused by the Dabie bandavirus (commonly known as SFTS virus, or SFTSV). SFTSV-induced immunosuppression during infection renders patients highly susceptible to invasive pulmonary aspergillosis. SFTS-associated pulmonary aspergillosis (SAPA) presents major therapeutic challenges and is linked to drastically worsened outcomes, including high mortality. This report aims to highlight the diagnostic and therapeutic challenges of SAPA and emphasize the value of early diagnosis using metagenomic next-generation sequencing (mNGS). CASE REPORT We report a case of a previously healthy 56-year-old male farmer admitted with SFTS. On hospital day 3, when only mild cough had begun, mNGS of both blood and sputum concurrently detected Aspergillus fumigatus alongside SFTSV. This very early, pre-radiographic diagnosis prompted immediate targeted therapy with voriconazole and favipiravir. Despite this, imaging showed progressive pulmonary infiltrates with cavitation. The clinical course was further complicated by severe acute respiratory syndrome coronavirus 2 co-infection, but the patient recovered with intensive care and was discharged on day 24. A review of 13 literature-reported SAPA cases revealed a mortality rate of 30.77% (4/13). CONCLUSIONS SAPA is a severe, rapidly progressive complication of SFTS with high mortality, typically emerging 1-2 weeks after onset. This case highlights the importance of early diagnosis using rapid methods such as mNGS and the need for timely antifungal intervention to improve patient outcomes. Early antifungal therapy in high-risk patients is crucial.},
}

Humans
Male
Middle Aged
*Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications
China
*Pulmonary Aspergillosis/diagnosis/complications
Farmers
COVID-19
Coinfection
Aspergillus fumigatus/isolation & purification
Antifungal Agents/therapeutic use

@article {pmid42134120,
year = {2026},
author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S},
title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.},
journal = {Food chemistry},
volume = {518},
number = {},
pages = {149574},
doi = {10.1016/j.foodchem.2026.149574},
pmid = {42134120},
issn = {1873-7072},
abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.},
}

@article {pmid42134135,
year = {2026},
author = {Huang, Z and Wang, J and Yang, C and Lv, Z and Wang, R},
title = {Integrated transcriptomics and metagenomics analyze the dynamic correlations between cecal mucosal tissue and cecal microbiota in Liangshan Yanying chickens during early postnatal development.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {106904},
doi = {10.1016/j.psj.2026.106904},
pmid = {42134135},
issn = {1525-3171},
abstract = {Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380-4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n = 10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14-28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.},
}

@article {pmid42134217,
year = {2026},
author = {Hua, Y and Xue, Y and Li, Z and Zhang, Y and Liu, Q and Liu, L and Tang, J},
title = {Effect of microplastics on arsenic transport in shallow groundwater of coastal transition zones.},
journal = {Water research},
volume = {301},
number = {},
pages = {126097},
doi = {10.1016/j.watres.2026.126097},
pmid = {42134217},
issn = {1879-2448},
abstract = {Coastal transition zones (CTZs) are dynamic zones where seawater intrusion and freshwater discharge interact. Arsenic (As) is a common contaminant in these zones, however its co-transport with increasing abundance microplastics (MPs) remains unclear. In this study, saturated column experiments combined with Hydrus-1D modeling were used to investigate the co-transport of As with polystyrene (PS), polyethylene (PE), and polylactic acid (PLA). Increasing salinity inhibited As transport in the absence of MPs. Under the same salinity, MPs generally increased As breakthrough, following the order PS > PE > PLA. With salinity increased, PS maintained a slight promoting effect on As breakthrough, whereas PE and PLA exhibited reduced breakthrough under high-salinity conditions. Co-transport was most pronounced at an As:MP ratio of 1:2, although PLA showed a non-linear response and lower As mobility at 1:1. Simulated seawater intrusion indicated that ionic-strength fluctuations produced distinct release peaks. MPs further enhanced non-equilibrium As release during flushing. Metagenomic sequencing of samples from the 21-day experiment indicated that MPs altered the microbial communities and increased the relative abundance of several As-related genes (such as AS3MT and arsC), particularly in the PS treatment. These findings clarify the effects of MPs on As transport and support risk assessment for coastal groundwater systems.},
}

@article {pmid42134269,
year = {2026},
author = {Jiang, J and Liu, R and Shen, Y and Yin, Z and Li, Y},
title = {Mechanistic insights into antimony immobilization by sulfur-metabolizing microorganisms under alternating oxic-anoxic conditions.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142328},
doi = {10.1016/j.jhazmat.2026.142328},
pmid = {42134269},
issn = {1873-3336},
abstract = {Antimony (Sb), as a toxic heavy metal(loid) element, poses potential risks to the environment and human health. The migration and transformation of Sb in the environment are closely linked to the macronutrient sulfur. However, under alternating oxic-anoxic conditions, the roles of sulfur and sulfur-metabolizing microorganisms in Sb mobility remain unclear. This study systematically investigated the role of exogenous thiosulfate (S2O3[2-]) in Sb(V) immobilization and the underlying mechanisms by integrating microcosm incubations, speciation analyses, and genome-resolved metagenomic analyses. We found that during the oxic-anoxic-oxic transition, Sb(V) was immobilized under anoxic condition and was released under oxic condition. However, thiosulfate amendment significantly inhibited Sb release through facilitating the sulfur-dependent reduction of Sb(V) to Sb(III) and formation of Sb2O3 precipitates. Complete Sb(V) immobilization was achieved within 14 days, concurrently with the oxidation of S2O3[2-] to SO4[2-], indicating thiosulfate is the primary electron donor for microbial reduction of Sb(V). Key microorganisms, including Ramlibacter (Bin.5), Thiomonas (Bin.105), and Unclassified (Bin.112 and Bin.123), which harbor antimonate/arsenate respiratory reductase gene (arrA) and sulfur oxidation pathway (Sox system), drive the sulfur-dependent Sb immobilization, as evidenced by metagenome-assembled genomes (MAGs) results. These findings enhance our understanding of the coupled cycling of Sb and S in alternating oxic-anoxic environments and provide a potential approach for Sb remediation.},
}

@article {pmid42134371,
year = {2026},
author = {Govender, KN and Street, TL and Sanderson, ND and Leach, L and Morgan, M and Eyre, DW},
title = {Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101333},
doi = {10.1016/j.lanmic.2025.101333},
pmid = {42134371},
issn = {2666-5247},
abstract = {BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results.

METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus.

FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%.

INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation.

FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.},
}

@article {pmid42134579,
year = {2026},
author = {Zhao, C and Hu, Z and Wang, D and Xu, M and Hao, Z and Fu, C and Zhang, J and Zhuang, L},
title = {Metagenomic insights into the enhancement of doxycycline hydrochloride removal in constructed wetlands under moderate lead stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134878},
doi = {10.1016/j.biortech.2026.134878},
pmid = {42134579},
issn = {1873-2976},
abstract = {Constructed wetlands (CWs) serve as an important ecological barrier preventing contaminated water from entering surface waters and are frequently exposed to antibiotic-heavy metal co-contamination under real operating conditions. However, how heavy metal stress regulates antibiotic removal through microbial processes in CWs remains poorly understood. Here, CWs subjected to doxycycline hydrochloride (DOX) and lead (Pb) co-contamination were established to elucidate the effects of different Pb stress levels on DOX removal performance and the underlying microbial mechanisms. The results showed that DOX removal was maximized under moderate Pb stress (1 mg/L), reaching a highest removal efficiency of 95.8%. Consistent toxicity responses were observed, with moderate Pb exposure significantly reducing effluent biotoxicity, alleviating plant stress, and improving overall system stability. Mass balance analysis demonstrated that microbial transformation dominated DOX removal, accounting for over 79% of total removal. Metagenomic analyses further revealed the underlying microbial mechanisms, showing that moderate Pb stress reshaped microbial community structure, promoted the enrichment of key functional microorganisms, and increased the abundance of DOX degradation-related functional genes. Representative functional taxa included Sphingomonas, Propionibacterium, and Candidatus Woesearchaeota archaeon. In contrast, high Pb stress (10 mg/L) imposed strong metal toxicity that suppressed the activity and diversity of core functional microorganisms, resulting in reduced DOX degradation capacity accompanied by toxicity accumulation. Collectively, this study clarifies how heavy metal stress regulates antibiotic removal through microbial pathways in CWs, and provide a reference for understanding CWs performance under co-contamination.},
}

@article {pmid42134580,
year = {2026},
author = {He, J and Xiang, B and Xu, W and Pan, Z},
title = {Comparative study on microbial mechanisms of denitrification failure in AAO process and air-lift internal circulation process under ultra-low C/N ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134881},
doi = {10.1016/j.biortech.2026.134881},
pmid = {42134580},
issn = {1873-2976},
abstract = {Denitrification failure under low-carbon conditions limits biological nitrogen removal. This study compared the recovery performance of a conventional anaerobic-anoxic-oxic (AAO) process and an air-lift internal circulation reactor (AICR) after carbon supplementation, following long-term operation at ultra-low C/N (≈1). Batch experiments showed that the AICR initiated denitrification more rapidly than the AAO. At C/N = 7, the AICR removed 62% of nitrate nitrogen (NO3[-]-N) within 4.5 h, while the AAO removed only 43%. After 10 h, removal efficiencies reached 78% in the AICR and 69% in the AAO. The AICR also had higher adenosine triphosphate (ATP) levels and greater denitrification enzyme activities. Quantitative polymerase chain reaction (qPCR) confirmed that nirS and nosZ copy numbers in the AICR were approximately twice those in the AAO. Metagenomic analysis revealed distinct genomic architectures in the two systems. The AAO relied on a limited number of versatile strains carrying complete denitrification gene clusters. In contrast, the AICR harbored a distributed network where denitrification steps were partitioned among phylogenetically diverse and functionally specialized strains. These differences in community architecture were linked to the distinct flow regimes of the two reactors and corresponded to enhanced functional modularity and metabolic redundancy in the AICR, which contributed to its faster recovery under carbon fluctuations.},
}

@article {pmid42134588,
year = {2026},
author = {Chauhan, A and Santhiya, D and Sharma, JG},
title = {Microbial consortium driven degradation of mixed microplastics: systematic review on enzymes and omics-based insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134885},
doi = {10.1016/j.biortech.2026.134885},
pmid = {42134588},
issn = {1873-2976},
abstract = {Microplastics (MPs) are among the most persistent pollutants in the environment. Mixed polymer waste further complicates the remediation due to their toxic additives and heterogenous composition. Conventional remediation methods show limited efficiency, especially for mixed MPs. As a result, biological approaches, particularly microbial consortium mediated degradation is a promising alternative. It is gaining increasing attention due to their cooperative metabolism and ability to degrade multiple polymers simultaneously. This review summarizes recent advances in consortium-based degradation of mixed MPs. It compares existing studies and identifies key challenges in translating laboratory findings to real-world. This review further discusses enzymes involved in the degradation of major polymer constituting mixed MPs. In addition, the role of multi-omics approaches like metagenomics, meta-transcriptomics, metabolomics, and integrated systems biology is also highlighted to explain microbial-metabolite interaction, functional pathways, and degradation mechanisms. Further, this review proposed future research directions focusing on green and scalable technologies. These include green biosensors for real-time monitoring, agro based aerogels and biochar for microbial immobilization, and nano-bubble assisted systems to enhance degradation under economic real-world conditions.},
}

@article {pmid42134644,
year = {2026},
author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X},
title = {Antibiotic-mediated Gut Microbiota Depletion Partially Attenuates Methamphetamine-induced Reward and Linoleic Acid Metabolic Disturbance.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {111022},
doi = {10.1016/j.neuropharm.2026.111022},
pmid = {42134644},
issn = {1873-7064},
abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of it could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.},
}

@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.},
}

@article {pmid42120383,
year = {2026},
author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW},
title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42120383},
issn = {2041-1723},
support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Carrageenan/metabolism
*Ruminants/microbiology
Rumen/microbiology
Glycoside Hydrolases/metabolism/genetics
Feces/microbiology
Bacteria/metabolism/genetics/classification/isolation & purification
Seaweed/metabolism
Bacteroides/metabolism/genetics/isolation & purification
Metagenomics
Phylogeny

@article {pmid42120665,
year = {2026},
author = {Chen, LG and Zhou, L and Wang, BW and Javed, M and Liu, YF and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial assembly and metabolic restructuring following CO2 injection in subsurface oil reservoir.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02066-w},
pmid = {42120665},
issn = {2191-0855},
support = {Grant No. 42473082//National Natural Science Foundation of China/ ; No. 42173076//National Natural Science Foundation of China/ ; No. 52074129//the National Natural Science Foundation of China/ ; 21ZR1417400//the Natural Science Foundation of Shanghai/ ; JKJ01231714//the Fundamental Research Funds for the Central Universities of China/ ; },
abstract = {Carbon dioxide (CO2) injection into oil reservoirs is a well-established and promising strategy for enhancing oil recovery while simultaneously sequestering carbon, whose effectiveness is increasingly recognized to be influenced by microbial-mediated mechanisms and biogeochemical processes. However, the impact of CO2-injected and storage on functional microbial communities and their metabolic potential remains poorly understood. The study employed high-throughput sequencing to analyze the composition and diversity of microbial communities in produced water from three production wells with a long-term (> 20 years) history of CO2 injection and two adjacent water-flooding ones in Xinli Oilfield, China. The results showed that CO2-injected wells had significantly higher microbial diversity and distinct metabolic potential relative to the adjacent water-flooding wells. A metabolic difference in the archaeal communities towards hydrogenotrophic and heterotrophic metabolisms, alongside an enrichment of bacterial taxa associated with sulfur and nitrogen cycling was observed. Correlation analysis revealed that microbial differentiation was strong associated with geochemical alteration (especially pH and some inorganic ions), with NH4[+] and S[2-] identified as key factors in this process. Metagenomic analysis based on high-quality metagenome-assembled genomes (MAGs) further demonstrated that CO2 injection led to a different profile of microbial metabolic functions relative to the water-flooding condition, characterized by significantly enhancing hydrogenotrophic methanogenesis, dissimilatory sulfate reduction, and denitrification, while diminishing methylotrophic methanogenesis and Wood-Ljungdahl pathway activity. These findings provide new insights into the microbial mechanisms driving carbon transformation in CO2-flooded oil reservoirs.},
}

@article {pmid42120930,
year = {2026},
author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X},
title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51805-3},
pmid = {42120930},
issn = {2045-2322},
support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; },
abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.},
}

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04958-7},
pmid = {42121077},
issn = {1471-2377},
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

@article {pmid42121260,
year = {2026},
author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E},
title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02369-x},
pmid = {42121260},
issn = {2049-2618},
support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; },
abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.

RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.

CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.},
}

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02410-z},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

@article {pmid42121750,
year = {2026},
author = {Moharam, I and Brüggemann, J and Schmitt, F and Schade, B and Böhm, B and Kappe, E and Emmrich, F and Najar, FZ and El-Mayet, FS},
title = {Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091331},
pmid = {42121750},
issn = {2076-2615},
abstract = {Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting-stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity.},
}

@article {pmid42121788,
year = {2026},
author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L},
title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091369},
pmid = {42121788},
issn = {2076-2615},
support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; },
abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.},
}

@article {pmid42122064,
year = {2026},
author = {Hussain, A and Abbas, Q and Nadeem, M and Nazar, A and Athar, A and Rahman, HUU},
title = {Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/diagnostics16091360},
pmid = {42122064},
issn = {2075-4418},
abstract = {Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4-104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future.},
}

@article {pmid42122249,
year = {2026},
author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI},
title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.},
journal = {Cancers},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/cancers18091453},
pmid = {42122249},
issn = {2072-6694},
support = {No Grant Number//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.},
}

@article {pmid42122826,
year = {2026},
author = {Pardo, JM and Suwannarach, N and Malichan, S and Cuellar, WJ and Siriwan, W},
title = {Mixed-Pathogen Infections in Vegetatively Propagated Crops: From Biological Synergism to Integrated Management.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/plants15091332},
pmid = {42122826},
issn = {2223-7747},
support = {000//Ministry of Higher Education, Science, Research and Innovation/ ; 000//Kasetsart University/ ; CROP-2023-157//Australian Centre for International Agricultural Research/ ; 000//National Research Council of Thailand/ ; },
abstract = {Vegetatively propagated crops, including cassava, sweet potato, banana, and potato, are susceptible to mixed-pathogen infections resulting from the continuous use of clonal planting material and infrequent seed replacement. A diverse array of viruses, bacteria, and fungi can accumulate within these materials over successive cultivation cycles, precipitating seed degeneration and complex disease syndromes that complicate diagnosis and management. Mixed infections frequently trigger synergistic interactions that exacerbate disease severity and yield losses. This review synthesizes data on mixed-pathogen complexes in vegetatively propagated crops, with particular focus on vascular and systemically colonizing pathogens and analyzing starch crops to highlight the epidemiological, biological, and ecological drivers of synergism and antagonism. Furthermore, the review examines host defense responses during coinfection, including the modulation of plant immune pathways, and evaluates how interpathogen dynamics influence pathological outcomes. Although advancements in molecular diagnostics-notably next-generation sequencing and metagenomics-have revolutionized the detection of mixed infections, they have also introduced challenges in differentiating causal agents from commensal microorganisms. Finally, we discuss the implications for integrated disease management, emphasizing clean seed systems, resistance breeding, and phenotyping strategies tailored to multipathogen environments. The dynamics of mixed infections is critical for resilient and sustainable management strategies amidst increasingly complex agricultural and climatic shifts.},
}

@article {pmid42122957,
year = {2026},
author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ},
title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093225},
pmid = {42122957},
issn = {2077-0383},
abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.},
}

@article {pmid42123237,
year = {2026},
author = {Liu, JW and Ma, X and Qian, YT and Wang, JW and Zhu, CY and Ma, DL},
title = {Detection of Nontuberculous Mycobacterial Skin Infection by Next-Generation Sequencing: A Pilot Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093504},
pmid = {42123237},
issn = {2077-0383},
support = {2022- PUMCH-161//National High Level Hospital Clinical Research Funding/ ; 3332024006//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Background: Nontuberculous mycobacteria (NTM) skin infections pose significant diagnostic challenges in clinical practice, due to nonspecific clinical/histopathological features and limitations of conventional pathogenic detection methods. Metagenomic next-generation sequencing (mNGS) offers a promising approach but requires further evaluation. Methods: A prospective pilot study at Peking Union Medical College Hospital enrolled 20 patients with cutaneous NTM infection, confirmed by positive skin culture or mNGS. All patients underwent thorough clinical assessment, skin biopsy for histopathology and culture, and mNGS testing of skin tissue. Treatment was based on identified species and disease extent. Treatment outcomes were tracked. Results: Among 20 patients (median age 45.5 years), fingers were the most common site affected (n = 10), followed by forearms (n = 7), hands (n = 4), and face (n = 4). Mycobacterium marinum was the predominant pathogen (n = 12), associated with fish bone puncture, followed by M. abscessus (n = 4). mNGS demonstrated a substantially higher positivity rate than culture (95% [19/20] vs. 30% [6/20]) and delivered results faster. Histopathology revealed granulomatous inflammation in all cases. Nineteen patients presented with non-disseminated disease; one immunocompromised patient (GATA2 deficiency) had disseminated M. abscessus infection. Treatment success was achieved in 17 patients (85%) with tailored antibiotic regimens. Adverse drug effects occurred in seven patients. Conclusions: In this pilot study of cutaneous NTM infections, mNGS enabled more rapid diagnosis relative to conventional culture. Clinical presentation and exposure history correlate with specific NTM species. Integrating mNGS with clinical assessment significantly improves diagnosis and management.},
}

@article {pmid42123326,
year = {2026},
author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS},
title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093741},
pmid = {42123326},
issn = {1422-0067},
mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; },
abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.},
}

Animals
Chickens/microbiology
*Manure/microbiology
*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Metagenome
Microbiota/genetics
Biodiversity

@article {pmid42123473,
year = {2026},
author = {Cheng, R and Liu, T and Liao, C and Wu, X and Zhu, L and Zhang, S},
title = {Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093891},
pmid = {42123473},
issn = {1422-0067},
support = {No. 32401056//National Natural Science Foundation of China/ ; 2024RC3144//Hunan Province Science and Technology Innovation Program/ ; },
mesh = {*Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Humans ; Molecular Sequence Annotation ; },
abstract = {Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening "sequence-function gap" exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function.},
}

*Proteins/chemistry/metabolism
*Computational Biology/methods
Databases, Protein
Humans
Molecular Sequence Annotation

@article {pmid42123477,
year = {2026},
author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M},
title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093893},
pmid = {42123477},
issn = {1422-0067},
mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; },
abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.},
}

Humans
*Mineral Waters/therapeutic use
Balneology/methods
Animals
Skin/drug effects

@article {pmid42123517,
year = {2026},
author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ},
title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093935},
pmid = {42123517},
issn = {1422-0067},
support = {10180//United States Department of Agriculture/ ; },
mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration & dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; },
abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.},
}

Humans
*Saliva/microbiology/drug effects
Female
Male
*Vaccinium macrocarpon/chemistry
*Polyphenols/pharmacology/administration & dosage/chemistry
*Microbiota/drug effects
Adult
Propylthiouracil
*Plant Extracts/pharmacology/chemistry/administration & dosage
*Photinia/chemistry
Taste/drug effects
*Mouthwashes/pharmacology/chemistry
*Fruit and Vegetable Juices
Young Adult

@article {pmid42124595,
year = {2026},
author = {Mejía-Pitta, A and Zhang, Z and Hossain, AA and Bartosik, K and Baca, CF and Peralta, C and Molina, H and Teplova, M and Brady, SF and Micura, R and Patel, DJ and Marraffini, LA},
title = {A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.25.707755},
pmid = {42124595},
issn = {2692-8205},
abstract = {The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.},
}

@article {pmid42125129,
year = {2026},
author = {Khantsi, M and Babalola, OO},
title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {},
pages = {e70157},
pmid = {42125129},
issn = {2575-6265},
abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.},
}

@article {pmid42125266,
year = {2026},
author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Devarajan, AK and Petrich, C and O'Sadnick, M and Tiirik, K and Truu, J},
title = {Microbial succession and hydrocarbon-degrading potential in Arctic sea ice exposed to dispersed crude oil and chemical dispersant.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag022},
pmid = {42125266},
issn = {2633-6685},
abstract = {The increasing oil exploration and transport activities in the Arctic amplify the risk of oil spills in ice-containing marine environments. Chemical dispersants, intended to promote oil biodegradation by breaking hydrocarbons into small droplets, are potential tools in cold marine oil spill mitigation; however, their fate and effectiveness within sea ice remain uncertain. This study examined the influence of dispersed crude oil and the chemical dispersant (FinasolOSR 51) on microbial community dynamics and hydrocarbon-degrading potential compared to clean ice during an 89-day sea-ice mesocosm experiment using shotgun metagenomics and metagenome-assembled genomes. Dispersant addition markedly reshaped microbial communities in both dispersed-oil and dispersant containing ice, causing similar shifts toward psychrophilic hydrocarbon degraders such as Oleispira, Bermanella, and Pseudoalteromonas. Although aliphatic hydrocarbon degradation genes were enriched, several dominant taxa exhibited limited hydrocarbon metabolic capacity yet possessed extensive stress-response traits. Oil hydrocarbon loss in ice remained modest despite the presence of degraders, likely due to the very low microbial abundance. These findings demonstrate that dispersants can strongly shape microbial communities in Arctic sea ice, without necessarily enhancing the biodegradation of oil hydrocarbons. This highlights the need for careful evaluation of dispersants as remediation tools in ice-containing Arctic marine environments.},
}

@article {pmid42125370,
year = {2014},
author = {, },
title = {Schmallenberg virus: State of Art.},
journal = {EFSA journal. European Food Safety Authority},
volume = {12},
number = {5},
pages = {3681},
pmid = {42125370},
issn = {1831-4732},
abstract = {This scientific report provides an overview of all research carried out on Schmallenberg virus (SBV), reviewing the current knowledge on SBV regarding genotyping findings, susceptible species, pathogenesis, transmission routes, immunity, seroprevalence, geographical and temporal SBV spread, improved within-herd transmission model, SBV impact assessment and within-herd and regional spread models. Metagenomic analysis identified SBV as a novel orthobunyavirus emerged in 2011 and it has been detected in domestic cattle, sheep, goats and 12 wild species. Seroprevalence studies indicate that SBV has probably spread over the whole of Europe, showing high seroprevalence at national scale, while larger variability is observed at regional scales. Clinical disease frequency is low and experimental infection on pregnant ewes and cows suggest that SBV rarely induces malformations. SBV may be detected from semen with a low frequency though there is no scientific evidence of transmission through insemination. Vector competence studies suggest that Culicoides are likely to be able to transmit SBV but found no evidence that mosquitoes are likely to be able to transmit it. SBV vertical transmission has not yet been identified as a major route. SBV has successfully overwintered, despite lengthy period of minimal vector activity and duration of immunity in cattle lasts for at least one year. A farm-to-farm spread model for SBV shows a rapid spread of infection across the study region and latent period, duration of viraemia, probability of transmission from host to vector and virus replication are sufficient to account for the rapid SBV spread. The between-farm SBV transmission model indicates that the application of movement restrictions has little effect on SBV spread. An impact assessment based on limited data suggests a probable effect of SBV infection on abortion, short gestation, non-return and the number of artificial inseminations required per animal. International trade restrictions by third countries represent the main SBV impact.},
}

@article {pmid42125413,
year = {2026},
author = {Wang, J and Qiu, J and Zhang, C},
title = {Crusted scabies complicated by septic shock: a fatal case report with incidental detection of Sarcoptes scabiei DNA in peripheral blood.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02577},
pmid = {42125413},
issn = {2214-2509},
abstract = {Crusted scabies is a severe form of scabies characterized by massive mite burden and profound immune dysregulation. Secondary bacterial infection is common and may progress to sepsis with fatal outcomes. We report a fatal case of crusted scabies complicated by septic shock in a 58-year-old man with diabetes mellitus and chronic dermatitis. The patient presented with diffuse erythroderma, extensive hyperkeratotic crusts, and deep skin fissures, and several household members had similar pruritic skin lesions. Laboratory investigations revealed marked eosinophilia, extremely elevated serum immunoglobulin E levels, and multiorgan dysfunction. Peripheral blood metagenomic next-generation sequencing identified multiple bacterial pathogens and incidentally detected Sarcoptes scabiei DNA. Despite broad-spectrum antimicrobial therapy, antiparasitic treatment, and intensive supportive care, the patient deteriorated and died. This case highlights crusted scabies as a potentially lethal condition when complicated by severe bacterial infection and underscores the need for cautious interpretation of parasitic DNA detected in blood, particularly in non-invasive ectoparasitic diseases.},
}

@article {pmid42125597,
year = {2026},
author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK},
title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112791},
pmid = {42125597},
issn = {2352-3409},
abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.},
}

@article {pmid42125669,
year = {2026},
author = {Szaraz, D and Bohm, J and Machacek, C and Salokova, G and Gachova, D and Ruzicka, F and Danek, Z and Gheit, T and Zavadil, J and Borilova Linhartova, P},
title = {Bacteriome-based oral dysbiosis index in patients with oral squamous cell carcinoma.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2668149},
pmid = {42125669},
issn = {2000-2297},
abstract = {BACKGROUND: Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs other oral samples and evaluate the association of a novel bacteriome-based Oral Dysbiosis Index (bbODI) with the OSCC surface.

MATERIALS AND METHODS: This pilot observational study used 84 patient-matched samples from the OSCC tumoral surface (swabs and biopsies), healthy oral mucosa (tongue and buccal swabs), and supragingival dental plaque swabs. Bacteriomes were analyzed by 16S rRNA amplicon sequencing. The presence of microscopic fungi and selected viruses was also evaluated.

RESULTS: The relative abundance of the genus Fusobacterium, the ratio of the relative abundances of gram-negative to gram-positive bacterial genera, and the bbODI on the tumour surface significantly differed from patient-matched healthy oral mucosa (both buccal and tongue swabs) and supragingival dental plaque samples. Oral candidosis was found in 25% of patients; all patients were negative for cytomegalovirus and Epstein-Barr virus.

CONCLUSIONS: Certain characteristics of the bacteriome composition of the OSCC surface differ from patient-matched samples of healthy oral mucosa and supragingival dental plaque. The proposed bbODI appears to be a promising non-invasive tool for the identification of bacteriome disruption on the OSCC surface.},
}

@article {pmid42125783,
year = {2026},
author = {Hu, X and Han, L and Ochoa-Hueso, R and Song, J and Yang, X and Wang, G},
title = {From Microbes to Molecules: Biodegradable Microplastics Reshape Soil Carbon Metabolism and Composition of Dissolved Organic Matter.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01030},
pmid = {42125783},
issn = {1520-5118},
abstract = {Microplastics (MPs) are ubiquitous in the environment, yet how conventional MPs (CMPs) and biodegradable MPs (BMPs) alter microbial carbon (C) metabolism and dissolved organic matter (DOM) remains unclear. Using metagenomic sequencing and Fourier transform ion cyclotron resonance mass spectrometry, we found that BMPs altered microbial C cycling profiles more profoundly than CMPs. This was driven by a significant enrichment of functional genes involved in aerobic respiration, C fixation, intracellular C decomposition, and fermentation. In addition, BMPs exerted stronger influences on prokaryotic and viral community structures than CMPs. Notably, BMPs specifically enriched unique microbial taxa and virus-host linkages carrying diverse C-cycling genes, coregulating key metabolic pathways, and promoting a "viral shuttle" mechanism that accelerated DOM turnover. These effects were mediated through enhanced accumulation of labile and recalcitrant C components in relation to fertilization regimes. These findings revealed mechanisms by which BMPs reshape soil carbon dynamics through microbial-viral interactions.},
}

@article {pmid42125851,
year = {2026},
author = {Fisher, CJ and Khrongsee, P and Subramaniam, K and Pushinsky, AD and Stevenson, V and Crawford, C and Goncalves, R},
title = {Acute Respiratory Distress Syndrome in a Dog With Canine Respiratory Coronavirus Infection.},
journal = {Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)},
volume = {},
number = {},
pages = {},
doi = {10.1111/vec.70113},
pmid = {42125851},
issn = {1476-4431},
abstract = {OBJECTIVE: To describe the clinical progression of acute respiratory distress syndrome (ARDS) associated with canine respiratory coronavirus and suspected aspiration in a previously healthy young dog.

CASE SUMMARY: A 1.5-year-old neutered male Rottweiler was presented for acute respiratory distress. The dog had a productive cough 2 weeks prior that was reported to have improved. While at a boarding facility, the dog developed decreased appetite and lethargy, regurgitated, and became acutely dyspneic. The dog was taken to the veterinarian on site, where thoracic radiographs revealed severe consolidation of the cranioventral lung lobes. The dog was presented to a university referral hospital approximately 12 h after regurgitation with fever, hypotension, hypoglycemia, and leukopenia, and was treated with positive pressure ventilation after failing high-flow oxygen therapy. The dog remained profoundly hypoxemic, developed acute kidney injury, and was euthanized after 24 h. Necropsy revealed diffuse alveolar damage consistent with a diagnosis of ARDS. Bacterial cultures were negative. Real-time polymerase chain reaction results from upper respiratory and fresh lung samples, as well as metagenomics analysis from a lung sample, confirmed the presence of canine respiratory coronavirus.

Canine respiratory coronavirus is primarily associated with mild upper respiratory signs and has not been previously associated with ARDS. Direct pulmonary damage from the virus, decreased mucociliary clearance secondary to viral ciliary damage followed by aspiration, and secondary pulmonary damage from systemic inflammation and coagulation disturbances are all possible in this case. The practical use of metagenomics, an emerging diagnostic screening tool that provides characterization of a virus's entire genome, is also demonstrated here. Metagenomics has not been previously described in small animal clinical medicine and may aid in surveillance of infectious canine respiratory disease and provide better understanding of the role of "milder" pathogens in patients with multifactorial respiratory failure.},
}

@article {pmid42126224,
year = {2026},
author = {Abuah, CY and Sipes, K and Buongiorno, J and Steen, AD and Bradley, JA and Giovannelli, D and Abramov, A and Peters, SL and Giannone, RJ and Hettich, RL and Liang, R and Boike, J and Vishnivetskaya, TA and Lloyd, KG},
title = {Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0045626},
doi = {10.1128/spectrum.00456-26},
pmid = {42126224},
issn = {2165-0497},
abstract = {The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches-metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics-we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass-remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.IMPORTANCEPermafrost thaw may be a critical climate feedback because microbial degradation of organic matter (OM) can release greenhouse gases. While fjords serve as major carbon burial sites, our results show that burial of terrestrial-derived OM in these sediments does not ensure protection from microbial degradation. Microbial communities in both active layer soils and fjord sediments harbor a broad arsenal of carbohydrate-active enzymes, with evidence of activity across diverse taxa. This functional continuity indicates that once terrestrial material is washed into fjords, it remains vulnerable to microbial breakdown despite different environmental conditions. Understanding these cross-system continuities in microbial function is essential for predicting the fate of OM in a rapidly warming Arctic and highlights the importance of including fjord sediments in global carbon cycle models.},
}

@article {pmid42126240,
year = {2026},
author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Javornik Cregeen, SJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW},
title = {Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0054726},
doi = {10.1128/aem.00547-26},
pmid = {42126240},
issn = {1098-5336},
abstract = {Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exist in the realm of wastewater-based viral epidemiology (WBE) for cancer-causing viruses, with existing studies using targeted approaches (i.e., PCR-based approaches) that lack genomic resolution. In this study, we used a hybrid-capture approach to detect, filter, and sequence all known oncogenic virus signals from wastewater samples collected over 3 years (May 2022-May 2025) in 16 Texas cities, covering nearly 25% of the state's population. Once sequenced, we used custom computational tools designed for wastewater metagenomics to assign reads into their respective virus of origin, estimate viral abundances over time, and measure genomic read coverage. Our data indicate that we successfully detected oncogenic viruses, including six known oncogenic viruses, and three suspected oncogenic viruses, across all sampling locations within Texas. We observed a gradual increase in the viral abundance of oncogenic viruses over 3 years, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as human papillomavirus (HPV) and Epstein-Barr virus (EBV) rose, with sharp increases in viral abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using this hybrid-capture technique for nearly all oncogenic viruses, with resolution down to the species and type taxonomic levels in some cases, such as that of HPV. Our study showcases the utility of hybrid-capture techniques to detect and track multiple oncogenic viruses simultaneously.IMPORTANCECancer-causing viruses are of major clinical significance, responsible for nearly 20% of all recorded cancer incidences in humans worldwide. There is a need for improved detection, tracking, and control of oncogenic viruses across the globe. To our knowledge, this work is the first comprehensive WBE approach used to detect all known oncogenic viruses concurrently, demonstrating the feasibility of monitoring the presence and levels of cancer-causing viruses and enabling the possibility of public health interventions in the future. Using this method, we obtain broad genomic coverage at strong depth and specificity, coupled with consistent real-time tracking dynamics of multiple oncogenic viruses. Furthermore, we showcase the ability to identify genomic regions on viral reference genomes from which sequenced reads originate. This information can be an invaluable tool toward understanding the viral prevalence dynamics in general populations, their relationship to cancer incidences in humans, and their mechanisms of viral evolution, including mutations.},
}

@article {pmid42126253,
year = {2026},
author = {Hambücken, L and Sudianto, E and Verleyen, E and Saw, JH and Baurain, D and Cornet, L},
title = {An early diverging SQR enzyme in Antarctic Gloeobacterales indicates sulfide tolerance in thylakoid-lacking cyanobacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042326},
doi = {10.1128/spectrum.00423-26},
pmid = {42126253},
issn = {2165-0497},
abstract = {Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions-characterized by sulfidic, anoxic oceans-posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of a sulfide-quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage. Phylogenetic analyses consistently position these SQR sequences at the base of the cyanobacterial clade, likely predating the multiple lateral transfers reported for this gene in the phylum. Additional searches in metagenomic data sets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions.IMPORTANCEThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic), a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an early diverging cyanobacterium lacking thylakoids, isolated from Antarctica, suggests that oxygenic and anoxygenic photosynthesis coexisted early on in cyanobacterial evolution. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.},
}

@article {pmid42126918,
year = {2026},
author = {Smith, DB and Simmonds, P and Siddell, SG},
title = {Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist.},
journal = {The Journal of general virology},
volume = {107},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002243},
pmid = {42126918},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Virology ; *Classification/methods ; Terminology as Topic ; },
abstract = {Just over 125 years has passed since the 'filterable' agents of tobacco mosaic disease and foot-and-mouth disease were first described as infectious, replicating entities smaller than bacteria. Today, viruses are formally classified into more than 16,000 species ranked into genera, families and higher taxa. The development of an official virus taxonomy has been overseen by an International Committee, first constituted in 1966 and renamed as the International Committee on Taxonomy of Viruses (ICTV) in 1975. Despite the engagement of the ICTV in virus taxonomy over the last 60 years, many aspects of virus classification and nomenclature may seem odd or sometimes incomprehensible to virologists more familiar with the taxonomy of cellular organisms. Who runs the ICTV? What are virus species demarcation criteria? Why have all virus species names become binomial? How can a sequence in a metagenomic dataset be assigned to a virus species? This article attempts to answer several such questions and outlines how a large, inclusive and global community of virologists has developed new and responsive policies for virus taxonomy in a decade when the pace of virus discovery has dramatically accelerated.},
}

*Viruses/classification/genetics
*Virology
*Classification/methods
Terminology as Topic

@article {pmid42127418,
year = {2026},
author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC},
title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag124},
pmid = {42127418},
issn = {1751-7370},
abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.},
}

@article {pmid42127818,
year = {2026},
author = {Mahler, M and Yuping, L},
title = {Predicting phage anti-defenses that shoot the messenger.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {811-813},
doi = {10.1016/j.chom.2026.04.014},
pmid = {42127818},
issn = {1934-6069},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Viral Proteins/metabolism/genetics ; Metagenomics ; Signal Transduction ; },
abstract = {Locked in a constant arms race, bacteria and their phage predators have evolved various defenses and counter-defenses. Compared to the numerous identified defenses, phage-encoded counter-defenses are understudied. In a recent Science paper, Tal et al. developed a structure-guided approach to identify phage proteins counteracting nucleotide signaling defenses using metagenomic data.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*Viral Proteins/metabolism/genetics
Metagenomics
Signal Transduction

@article {pmid42127820,
year = {2026},
author = {Bickel, S and Berg, G},
title = {Microbial diversity creates a global firewall against pathogens in soil.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {817-819},
doi = {10.1016/j.chom.2026.04.016},
pmid = {42127820},
issn = {1934-6069},
mesh = {*Soil Microbiology ; Humans ; Metagenomics ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Melioidosis/microbiology ; *Microbiota ; Tuberculosis/microbiology ; Soil ; Animals ; },
abstract = {Soil is a critical ecological contributor to plant and animal health. In this issue of Cell Host & Microbe, Xiong et al. use global metagenomic data to show that human pathogens linked to diseases like tuberculosis, melioidosis, and sepsis are widespread in humid and agricultural soils harboring reduced microbial diversity.},
}

*Soil Microbiology
Humans
Metagenomics
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Melioidosis/microbiology
*Microbiota
Tuberculosis/microbiology
Soil
Animals

@article {pmid42127824,
year = {2026},
author = {Bouzek, DC},
title = {What the nose knows of cystic fibrosis microbes and hypertonic saline.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {827-829},
doi = {10.1016/j.chom.2026.04.017},
pmid = {42127824},
issn = {1934-6069},
mesh = {*Cystic Fibrosis/microbiology/drug therapy ; Humans ; Saline Solution, Hypertonic/pharmacology ; *Nasopharynx/microbiology ; *Microbiota ; Metagenomics ; Infant ; *Nose/microbiology ; },
abstract = {In this issue of Cell Host & Microbe, Steinberg et al.[1] present a microbial gene atlas of nasopharyngeal swabs in infants with cystic fibrosis and healthy controls using shotgun metagenomic sequencing. The impacts of clinical interventions on respiratory microbial function can be identified and experimentally validated using the atlas.},
}

*Cystic Fibrosis/microbiology/drug therapy
Humans
Saline Solution, Hypertonic/pharmacology
*Nasopharynx/microbiology
*Microbiota
Metagenomics
Infant
*Nose/microbiology

@article {pmid42127855,
year = {2026},
author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y},
title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {107056},
doi = {10.1016/j.psj.2026.107056},
pmid = {42127855},
issn = {1525-3171},
abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.},
}

@article {pmid42127905,
year = {2026},
author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y},
title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102797},
doi = {10.1016/j.xcrm.2026.102797},
pmid = {42127905},
issn = {2666-3791},
abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.},
}

@article {pmid42128151,
year = {2026},
author = {Yang, F and Sui, C and Tian, H and Ao, J},
title = {Metagenomic next-generation sequencing reveals the clinicopathological features of mucormycosis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108553},
doi = {10.1016/j.micpath.2026.108553},
pmid = {42128151},
issn = {1096-1208},
abstract = {BACKGROUND: Mucormycosis is a rare but highly lethal opportunistic infection driven by mucor fungi, which mainly affects individuals with compromised immune systems, such as diabetic patients and organ transplant recipients. This study aims to investigate the clinicopathological features of patients with mucormycosis diagnosed by metagenomic next-generation sequencing (mNGS).

METHODS: A systematic analysis was conducted in 15 cases of mucormycosis diagnosed and treated at Hunan Provincial People's Hospital between January 2019 and July 2024. Various detection methods were utilized, including hematoxylin-eosin staining, fungal fluorescence staining, fungal culture, and high-throughput mNGS technology to ensure an accurate diagnosis. Furthermore, we conducted a literature review and analyzed 311 cases of mucormycosis published in the public databases between 2021 and 2024 to assess the underlying pathological characteristics.

RESULTS: Of the 15 cases treated in our institute, ten (66.7%) were males, with a median age of 41 (range 4-78),five (33.3%) were females, with a median age of 58.5 (range 32-85). Compared to other detection methods including PAS/PASM staining, mNGS proved effective in diagnosing typical mucormycosis infections in 15 of the patients in this study. The literature review of 311 cases indicated that the lungs and bronchi were the main sites of infection, followed by the nasal cavity, brain, and skin. Diabetes emerged as the most prevalent underlying condition, present in more than 40% of cases. Other internal and immune system disorders, such as immunodeficiency disease, were also associated with an increased risk of infection.

CONCLUSIONS: MNGS is an effective diagnostic tool for mucormycosis.},
}

@article {pmid42128673,
year = {2026},
author = {, and , and , },
title = {[Expert consensus on laboratory identification of emerging pathogens based on metagenomic next-generation sequencing technology(2025 edition)].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {5},
pages = {669-684},
doi = {10.3760/cma.j.cn112150-20251117-01086},
pmid = {42128673},
issn = {0253-9624},
support = {2024ZD0532804//National Science and Technology Major Special Project for Noncommunicable Chronic Diseases/ ; 2025ZD01903400//National Science and Technology Major Special Project for Prevention and Control of New Emergencies and Major Infectious Diseases/ ; 2025-I2M-KJ-001, 2025-I2M-XHJC-004//CAMS Innovation Fund for Medical Sciences(CIFMS)/ ; },
mesh = {*High-Throughput Nucleotide Sequencing ; *Metagenomics ; Humans ; Consensus ; *Communicable Diseases, Emerging/diagnosis ; Computational Biology ; },
abstract = {Emerging pathogen infections pose a significant challenge to global public health security. Pathogen metagenomic next-generation sequencing (mNGS), characterized by its hypothesis-free, culture-independent, and unbiased nature, provides a powerful tool for the timely detection and precise identification of emerging pathogens. This consensus was jointly developed by multidisciplinary experts from clinical laboratories, infectious diseases, disease prevention and control, and other relevant fields. It aims to standardize the identification process for clinically suspected emerging pathogen infections, as well as specimen submission, technical requirements, bioinformatic analysis, and reporting and interpretation procedures for the laboratory identification of emerging pathogens using clinical mNGS technology. This framework provides systematic guidance for clinical early warning and practice.},
}

*High-Throughput Nucleotide Sequencing
*Metagenomics
Humans
Consensus
*Communicable Diseases, Emerging/diagnosis
Computational Biology

@article {pmid42128675,
year = {2026},
author = {Zhou, HJ and Ma, JX and Hu, JR and Han, YX and Yang, B and Zhou, ZM and Li, LL and Liu, JY and Du, XL and Cui, ZG and Kan, B},
title = {[Analysis on the epidemiological characteristics of legionnaires' disease in China based on multi-source data].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {5},
pages = {714-720},
doi = {10.3760/cma.j.cn112150-20260306-00178},
pmid = {42128675},
issn = {0253-9624},
support = {GZNL2024A01025//Special Project of Guangzhou National Laboratory/ ; 2022YFC2305300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; China/epidemiology ; *Legionnaires' Disease/epidemiology/microbiology ; Male ; Middle Aged ; Aged ; Female ; Genotype ; High-Throughput Nucleotide Sequencing ; Legionella pneumophila ; Legionella/genetics ; Adult ; Incidence ; },
abstract = {Objective: To analyze the epidemiological characteristics of Legionnaires' disease in China based on multi-source data. Methods: Based on the metagenomic next-generation sequencing (mNGS) data of bronchoalveolar lavage specimens collected from a third-party medical testing institution from March 2024 to September 2025, this study aggregated nucleic acid detection data for multiple pathogens from the National Pathogenic Bacteria Identification Network's respiratory syndrome surveillance and conducted a meta-analysis by combining published literature. Descriptive epidemiological methods were used to analyze the demographic characteristics, spatiotemporal distribution, and Legionella species and genotype of Legionnaires' disease in China. Results: By integrating three types of data sources, a total of 1 866 Legionnaires' disease cases were included in the study. Chinese Legionnaires' disease patients were predominantly middle-aged and elderly males, accounting for 64.31% of cases. The age distribution of cases exhibited a bimodal pattern, with a significant concentration in the middle-aged and elderly population. The 60-65 age group had the highest incidence. However, in addition to the peak in the middle-aged and elderly population, there was also a peak in the 0-5 age group. The number of cases showed a peak occurring from July to August. The cases exhibited significant regional distribution disparities across the country. Legionella pneumophila infection was predominant (accounting for 95.70%), with other species including Legionella macleodii (20 cases) and Legionella longbeachae (18 cases). Among 412 samples, L. pneumophila genotypes were obtained, divided into 7 sequence types, including ST36 (n=148), ST1 (n=60), ST23 (n=58), ST51 (n=51), ST734 (n=51), ST42 (n=32), and ST47 (n=12). The distribution of STs in different geographical regions had commonalities, but there were also certain regional differences. The results of universal core genome multi-locus sequence typing showed that each ST formed relatively independent branch clusters, indicating clear genetic differentiation between different STs. The overall genetic diversity of Legionella in China was high. Conclusion: Legionella-positive cases have been detected throughout the year in China, with a wide distribution and regional differences. L. pneumophila has a high proportion and a large genetic diversity in its genome.},
}

Humans
China/epidemiology
*Legionnaires' Disease/epidemiology/microbiology
Male
Middle Aged
Aged
Female
Genotype
High-Throughput Nucleotide Sequencing
Legionella pneumophila
Legionella/genetics
Adult
Incidence

@article {pmid42114750,
year = {2026},
author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E},
title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28157},
pmid = {42114750},
issn = {1525-3198},
abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.},
}

@article {pmid42115187,
year = {2026},
author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X},
title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04095-2},
pmid = {42115187},
issn = {2158-3188},
abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.},
}

@article {pmid42115271,
year = {2026},
author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W},
title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52084-8},
pmid = {42115271},
issn = {2045-2322},
support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; },
abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.},
}

@article {pmid42115921,
year = {2026},
author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F},
title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05117-1},
pmid = {42115921},
issn = {1471-2180},
abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.},
}

@article {pmid42116123,
year = {2026},
author = {Zhou, J and Cheng, H and Zhang, Y and Liu, T and Chen, X and Lea-Smith, DJ and Todd, JD and Liu, J and He, X and Liu, R and Zhang, XH},
title = {Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00908-5},
pmid = {42116123},
issn = {2524-6372},
support = {BB/Y008332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/X014428//Natural Environmental Research Council/ ; NE/P012671//Natural Environmental Research Council/ ; RPG-2020-413//Leverhulme Trust/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2025YFF0516900&2025YFF0516903//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.

RESULTS: To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4[+] and SiO3[2-]) based on Pearson's correlation analysis.

CONCLUSION: This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.},
}

@article {pmid42116193,
year = {2026},
author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS},
title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00909-4},
pmid = {42116193},
issn = {2524-6372},
support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; },
abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.

METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.

RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.

CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.},
}

@article {pmid42116465,
year = {2026},
author = {Ozaki, GEDN and Maciel, ESO and Souza, BP and da Silva-Padilha, MP and Santos, NMMO and Oliveira, JCS and Souza, VB and Tulini, FL},
title = {Development and characterization of seriguela (Spondias purpurea) water kefir: metagenomic insights and functional potential of a spray-dried probiotic powder.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119194},
doi = {10.1016/j.foodres.2026.119194},
pmid = {42116465},
issn = {1873-7145},
mesh = {*Kefir/microbiology/analysis ; *Probiotics/analysis ; Powders ; Fermentation ; *Metagenomics ; *Spray Drying ; Food Microbiology ; Hydrogen-Ion Concentration ; Antioxidants/analysis ; Fruit/chemistry/microbiology ; Bacteria/classification/genetics ; },
abstract = {Water kefir is a fermented probiotic beverage suitable for those with lactose intolerance, dairy allergies, or vegan diets. Adding fruits during fermentation can modulate microbial dynamics, sensory attributes, and biochemical composition, thereby enhancing functional properties. In this context, Spondias purpurea (seriguela), a bioactive-rich fruit native to the Americas, represents a promising yet underexplored substrate for the development of functional beverages. Therefore, this study investigated the composition of seriguela and its application in water kefir production, followed by physicochemical and metagenomic characterization and the evaluation of spray-dried formulations. Seriguela fruits exhibited an acidic pH (3.63), the presence of coumarins, steroids, and tannins, and remarkable antioxidant activity. Seriguela-flavored kefir maintained microbial levels comparable to those of traditional kefir (7.1 and 6.8 log CFU/mL for bacteria and yeasts, respectively), promoting a predominance of Komagataeibacter saccharivorans, Acetobacter aceti, A. lovaniensis, Liquorilactobacillus mali, Clostridium pasteurianum, and yeasts from the Saccharomyces genus. This change in the microbiota of seriguela-flavored kefir indicates a more homogeneous fermentation with pronounced acetic characteristics and probiotic potential. Furthermore, the spray-dried kefir demonstrated good physical properties, remarkable resistance under simulated gastrointestinal conditions, and moderate stability during refrigerated storage throughout 30 days (75.7% and 82.9% of survival for bacteria and yeasts, respectively, enumerated on De Man, Rogosa & Sharpe agar and potato dextrose agar), highlighting its potential as a stable probiotic product. Overall, these results demonstrate the suitability of seriguela as a functional ingredient in water kefir and confirm spray-drying as a viable strategy for producing stable fermented powders with potential health-promoting properties.},
}

*Kefir/microbiology/analysis
*Probiotics/analysis
Powders
Fermentation
*Metagenomics
*Spray Drying
Food Microbiology
Hydrogen-Ion Concentration
Antioxidants/analysis
Fruit/chemistry/microbiology
Bacteria/classification/genetics

@article {pmid42116469,
year = {2026},
author = {Liu, D and Li, J and Zhang, J and Zhang, C},
title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119201},
doi = {10.1016/j.foodres.2026.119201},
pmid = {42116469},
issn = {1873-7145},
mesh = {*Carbon Dioxide/chemistry ; *Taste ; *Microbiota ; *Vegetables/microbiology/metabolism/chemistry ; *Food Microbiology ; *Atmosphere ; Biogenic Amines/analysis/metabolism ; Food Handling/methods ; Volatile Organic Compounds/analysis ; },
abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.},
}

*Carbon Dioxide/chemistry
*Taste
*Microbiota
*Vegetables/microbiology/metabolism/chemistry
*Food Microbiology
*Atmosphere
Biogenic Amines/analysis/metabolism
Food Handling/methods
Volatile Organic Compounds/analysis

@article {pmid42116470,
year = {2026},
author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W},
title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119200},
doi = {10.1016/j.foodres.2026.119200},
pmid = {42116470},
issn = {1873-7145},
mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Indoles/metabolism ; *Oligosaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Mice ; *Propionates/metabolism ; *Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy ; *Receptors, Aryl Hydrocarbon/metabolism ; *Anti-Bacterial Agents/adverse effects ; Humans ; Male ; Female ; Prospective Studies ; Dysbiosis/chemically induced ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.

OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.

METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.

RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.

CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.},
}

*NF-E2-Related Factor 2/metabolism
Animals
*Indoles/metabolism
*Oligosaccharides/pharmacology
Gastrointestinal Microbiome/drug effects
Mice
*Propionates/metabolism
*Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy
*Receptors, Aryl Hydrocarbon/metabolism
*Anti-Bacterial Agents/adverse effects
Humans
Male
Female
Prospective Studies
Dysbiosis/chemically induced
Oxidative Stress/drug effects
Multiomics

@article {pmid42116511,
year = {2026},
author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W},
title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119274},
doi = {10.1016/j.foodres.2026.119274},
pmid = {42116511},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; },
abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.},
}

*Fermentation
*Microbiota
*Metabolome
Food Microbiology
Taste
Volatile Organic Compounds/analysis
Bacteria/metabolism/classification/genetics
*Wine/microbiology/analysis
Fungi/metabolism/classification
Metabolomics
Flavoring Agents
China

@article {pmid42116518,
year = {2026},
author = {Zhou, H and Xu, B and Zhang, L and Yan, L and Wang, R and Xu, Q and Jiang, C and Chen, A and Wu, X and Li, X},
title = {Ecological dominance and genomic features of bacterial generalists during pit fermentation of three distinct baijiu types in Anhui Province.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119296},
doi = {10.1016/j.foodres.2026.119296},
pmid = {42116518},
issn = {1873-7145},
mesh = {*Fermentation ; China ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Wine/microbiology/analysis ; Lactobacillus/genetics/metabolism ; },
abstract = {Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.},
}

*Fermentation
China
*Food Microbiology
*Bacteria/genetics/classification/metabolism
*Wine/microbiology/analysis
Lactobacillus/genetics/metabolism

@article {pmid42116534,
year = {2026},
author = {Veyrenche, N and Boluda, S and Pérot, P and Malissin, I and Leruez-Ville, M and Jamet, A and Ferroni, A and Regnault, B and Salmona, M and Feghoul, L and Robert-Capraro, L and Leroux, A and Grasland, B and Niqueux, E and Briand, FX and Plu, I and Seilhean, D and Megarbane, B and Fourgeaud, J and Dheilly, NM},
title = {One Health Investigation into Fatal Encephalitis Caused by Pigeon Paramyxovirus Type 1, France.},
journal = {Emerging infectious diseases},
volume = {32},
number = {5},
pages = {753},
doi = {10.3201/eid3205.251576},
pmid = {42116534},
issn = {1080-6059},
mesh = {Humans ; France/epidemiology ; *Newcastle disease virus/genetics/classification/isolation & purification ; Fatal Outcome ; *Newcastle Disease/virology/diagnosis/epidemiology ; Animals ; Male ; Phylogeny ; Columbidae/virology ; *Encephalitis, Viral/diagnosis/virology/epidemiology ; },
abstract = {Pigeon paramyxovirus type 1 (PPMV-1) is a genotype of avian paramyxovirus type 1 that uses species of the family Columbidae as reservoir species. We report fatal PPMV-1 encephalitis in a human without immunosuppression or travel history outside metropolitan France. Postmortem analyses revealed PPMV-1 in tissues, underscoring that physicians should consider this potential diagnosis.},
}

Humans
France/epidemiology
*Newcastle disease virus/genetics/classification/isolation & purification
Fatal Outcome
*Newcastle Disease/virology/diagnosis/epidemiology
Animals
Male
Phylogeny
Columbidae/virology
*Encephalitis, Viral/diagnosis/virology/epidemiology

@article {pmid42116592,
year = {2026},
author = {Andreani, J and Boschi, C and Decoppet, A and Delerce, J and Penant, G and Karadeniz, A and Grimaldier, C and Jardot, P and Zangoli, L and Mandy, M and Vigroux, N and Polesso, F and Edouard, S and Cano, P and Lagier, JC and La Scola, B and Colson, P},
title = {Severe Respiratory Illness and Death Associated with Outbreak of Human Rhinovirus B14 among Older Adults, France, 2024.},
journal = {Emerging infectious diseases},
volume = {32},
number = {5},
pages = {768-773},
doi = {10.3201/eid3205.250981},
pmid = {42116592},
issn = {1080-6059},
mesh = {Humans ; France/epidemiology ; *Rhinovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; *Picornaviridae Infections/epidemiology/virology/mortality ; Aged ; Male ; Female ; Aged, 80 and over ; *Respiratory Tract Infections/epidemiology/virology/mortality ; Phylogeny ; Genome, Viral ; },
abstract = {We investigated an outbreak of unknown respiratory disease and 8 deaths among older adults in a long-term care facility in France. We identified human rhinovirus (HRV) by quantitative PCR and HRV-B14 by metagenomics. We obtained 5 HRV-B14 genomes that diverged from 5 publicly available genomes. Real-time metagenomics could enable rapid clinical diagnoses.},
}

Humans
France/epidemiology
*Rhinovirus/genetics/classification/isolation & purification
*Disease Outbreaks
*Picornaviridae Infections/epidemiology/virology/mortality
Aged
Male
Female
Aged, 80 and over
*Respiratory Tract Infections/epidemiology/virology/mortality
Phylogeny
Genome, Viral

@article {pmid42116727,
year = {2026},
author = {Kutter, JS and Cuevas-Lobato, O and Fernandez-Pacheco-Gonzalez-Echavarri, BE and Moreno-Gomila, C and Garcia-Ibañez, N and Camacho, J and Ruiz-Pedro, E and Cabrerizo, M and Alós, JI and Diez-Fuertes, F and Fernandez-Garcia, MD},
title = {Unraveling the Transmission Dynamics of a Novel Norovirus GII.17[P17] Lineage During Two Consecutive Outbreaks in a Spanish Hospital.},
journal = {Journal of medical virology},
volume = {98},
number = {5},
pages = {e70966},
doi = {10.1002/jmv.70966},
pmid = {42116727},
issn = {1096-9071},
support = {PI23CIII-00009//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Caliciviridae Infections/epidemiology/transmission/virology ; *Norovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; Spain/epidemiology ; Phylogeny ; *Cross Infection/epidemiology/virology/transmission ; Feces/virology ; *Genotype ; Male ; Female ; Middle Aged ; Adult ; Molecular Epidemiology ; Aged ; Hospitals ; High-Throughput Nucleotide Sequencing ; *Gastroenteritis/epidemiology/virology ; Young Adult ; Genome, Viral ; },
abstract = {Norovirus outbreaks in healthcare settings pose significant challenges to infection prevention and control (IPC). To prevent and control such outbreaks efficiently, identifying sources and transmission clusters (TCs) is crucial but often limited by traditional outbreak investigations. Here, we examined two consecutive hospital norovirus outbreaks employing a genomic epidemiology approach to elucidate transmission dynamics and guide IPC strategies. Stool samples of 54 symptomatic patients were analyzed with different diagnostic methods, and 26 norovirus-positive samples underwent metagenomic next-generation sequencing (mNGS) for phylodynamic and phylogenetic analyses. All infections belonged to the novel GII.17[P17] lineage, circulating globally since 2023/2024. LiquidArray® outperformed fluorescence immunoassay (FIA, 28.6%) and RT-PCR (85.7%) with FIA's low sensitivity leading to missed cases highlighting the need for molecular confirmation for accurate outbreak management. Genomic analysis revealed multiple introductions, with two TCs identified in Outbreak-1 and one in Outbreak-2, as well as inter-hospital-unit spread. Reconstruction of transmission trees indicated sustained person-to-person spread with 0-3 unobserved intermediate cases in both outbreaks. Identical sequences in patients without clear epidemiological links suggested possible fomite transmission. These analyses provided key insights into infection sources and TCs that would have remained unknown using epidemiological investigations alone, supporting more targeted IPC resource allocation and intervention strategies.},
}

Humans
*Caliciviridae Infections/epidemiology/transmission/virology
*Norovirus/genetics/classification/isolation & purification
*Disease Outbreaks
Spain/epidemiology
Phylogeny
*Cross Infection/epidemiology/virology/transmission
Feces/virology
*Genotype
Male
Female
Middle Aged
Adult
Molecular Epidemiology
Aged
Hospitals
High-Throughput Nucleotide Sequencing
*Gastroenteritis/epidemiology/virology
Young Adult
Genome, Viral

@article {pmid42116832,
year = {2026},
author = {Dawson, MN and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {189},
pmid = {42116832},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Aurelia sp. 4 Dawson et al., 2005 (moon jellyfish; Cnidaria; Scyphozoa; Semaeostomeae; Ulmaridae). The genome sequence has a total length of 462.10 megabases. Most of the assembly (99.99%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.88 kilobases. From the metagenome data, we recovered 3 bins, of which 2 were high-quality MAGs.},
}

@article {pmid42116847,
year = {2026},
author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA},
title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag081},
pmid = {42116847},
issn = {2730-6151},
abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.},
}

@article {pmid42117813,
year = {2026},
author = {Qi, W and Lü, L and Huang, K and Qi, J and Li, M and Shi, M and Wang, H},
title = {Effects of Rotary Tillage and Fertilization on Chemical Properties and Microbial Communities of Soil Under Continuous Morchella Mushroom Cultivation.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090674},
pmid = {42117813},
issn = {2079-7737},
support = {2024XTCX0403//Liaoning Academy of Agricultural Sciences Collaborative Innovation Project/ ; 2026NYGG010//Key Core Technology Research and Development in Shaanxi Province Agriculture/ ; },
abstract = {The severe continuous cropping obstacles in Morchella cultivation, driven primarily by soil microecological imbalance, critically constrain the sustainable development of the industry. To address this challenge, this study evaluated the efficacy of rotary tillage, calcium cyanamide (CaCN2), and organic fertilizer, applied individually and in combination, in mitigating these obstacles and explored the underlying microbial mechanisms. The soil was treated on 5 August 2024, and soil samples were collected on 5 October 2024. Four treatments were established: continuous cropping control (CK), rotary tillage (XGX), rotary tillage combined with calcium cyanamide (MPD), and rotary tillage combined with calcium cyanamide and organic fertilizer (MPX). Soil chemical properties were analyzed in conjunction with metagenomic sequencing to characterize the responses of soil properties and microbial communities, including both eukaryotic and bacterial taxa. The results indicated that the MPD treatment showed a relatively pronounced effect in enhancing key soil fertility indicators, including soil organic matter (OM), total nitrogen (TN), available nitrogen (AN), available potassium (AK), and total phosphorus (TP). All amendments significantly altered microbial community structures. Specifically, the integrated MPX treatment effectively reduced the relative abundance of the pathogenic fungus Olpidium while maintaining higher overall microbial diversity. It also significantly promoted the abundance of Morchella itself and beneficial bacterial phyla such as Actinomycetota and Pseudomonadota. Redundancy analysis identified AN and AK as the primary drivers of eukaryotic community variation, whereas Availa-ble phosphorus (AP) and potential of hydrogen (pH) were the key factors shaping the bacterial community. The results indicated that MPD was the showed relatively pronounced effectiveness in rapidly improving soil fertility and suppressing pathogenic fungi. In contrast, MPX showed relatively better performance in optimizing microbial community structure, enhancing microbial diversity, and strengthening overall ecological stability. These two treatments exhibited distinct advantages in soil chemical improvement and microbial community regulation, respectively, thereby providing alternative practical strategies and a theoretical basis for the ecological management of continuous-cropping obstacles in Morchella cultivation. It should be noted that this study did not include treatments with calcium cyanamide alone, organic fertilizer alone, or their combined application without rotary tillage. This is primarily because rotary tillage is a standard land preparation practice in Morchella cultivation, and the use of soil amendments without accompanying tillage is rarely adopted under practical production conditions.},
}

@article {pmid42118424,
year = {2026},
author = {Devi, P and Nath, SK and Barua, B and Saha, T},
title = {Big data and artificial intelligence in animal nutrition: a new era of precision feeding.},
journal = {Tropical animal health and production},
volume = {58},
number = {4},
pages = {},
pmid = {42118424},
issn = {1573-7438},
mesh = {Animals ; *Big Data ; *Artificial Intelligence ; *Animal Feed/analysis ; *Animal Husbandry/methods ; *Animal Nutritional Physiological Phenomena ; *Livestock/physiology ; Dairying/methods ; },
abstract = {The convergence of Big Data and Artificial Intelligence (AI) is redefining animal nutrition by enabling precision feeding systems that are individualized, data-driven, and sustainability-oriented. This review synthesizes recent advances in multi-omics technologies, sensor-based monitoring, and machine learning applications across feed formulation, health surveillance, and production optimization. Precision feeding in pigs has been shown to reduce production costs by more than 8%, decrease protein and phosphorus intake by approximately 25%, lower nutrient excretion by up to 40%, and reduce greenhouse gas (GHGs) emissions by 6%, while maintaining or improving performance. In dairy systems, precision feed management strategies have achieved approximately 9.7% lower dietary crude protein levels, 14% reductions in manure nitrogen excretion, and annual net income gains of USD 137 per cow. AI-driven models have enhanced prediction of milk yield, feed conversion ratio (R[2] = 0.74), and residual feed intake (R[2] = 0.76), while enabling 96.26% accuracy in detecting microplastics in poultry feed. Integration of genomic, phenotypic, and sensor-derived datasets supports real-time monitoring, with wearable and IoT technologies transforming livestock management through continuous tracking of feeding behavior, emissions, and welfare indicators. Despite significant progress, current systems remain constrained by data heterogeneity, limited interoperability, and insufficient prescriptive decision-support frameworks. This article identifies methodological, technological, and adoption-related gaps, while highlighting future directions including nutrigenomics- and metagenomics-informed diet design, adaptive precision nutrition, and cost-effective solutions for smallholder systems. Collectively, these innovations establish Big Data and AI-enabled precision nutrition as a cornerstone of sustainable livestock production, advancing food security, climate resilience, and ethical animal management.},
}

Animals
*Big Data
*Artificial Intelligence
*Animal Feed/analysis
*Animal Husbandry/methods
*Animal Nutritional Physiological Phenomena
*Livestock/physiology
Dairying/methods

@article {pmid42118429,
year = {2026},
author = {Tekin, B and Gurbanov, R},
title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42118429},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Aging/physiology
Biomarkers/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
Animals
Host Microbial Interactions
Fatty Acids, Volatile/metabolism

@article {pmid42119030,
year = {2026},
author = {Yu, J and Tang, SN and Lee, PKH},
title = {Host-Linked Virome Assembly and Turnover Predict Bacterial Community Structure in Wastewater Treatment Systems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag120},
pmid = {42119030},
issn = {1751-7370},
abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1,046 and 1,386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.},
}

@article {pmid42119140,
year = {2026},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13903},
pmid = {42119140},
issn = {1520-5851},
abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.},
}

@article {pmid42119184,
year = {2026},
author = {Pilliol, V and Beye, M and Boualam, MA and Tellissi, L and Slimani, A and Drancourt, M and Aboudharam, G and Tassery, H and Grine, G and Terrer, E},
title = {Evidence of a millennia-old association between a methanogenic archaeon and a bacterium in dental calculus: A re-analysis of ancient and modern metagenomic datasets.},
journal = {Archives of oral biology},
volume = {188},
number = {},
pages = {106622},
doi = {10.1016/j.archoralbio.2026.106622},
pmid = {42119184},
issn = {1879-1506},
abstract = {OBJECTIVES: Granehäll et al. (2021) identified TS-2 as an unknown Methanobrevibacter lineage abundant in ancient dental calculus, less prevalent in modern samples, and not linked to any cultivated representative. We aimed (i) to determine whether TS-2 corresponds to the cultivated oral archaeon Methanobrevibacter massiliense using genome-based species delineation, and (ii) to assess the antiquity of the association between M. massiliense and Pyramidobacter piscolens in ancient and modern dental calculus.

DESIGN: This fully in silico study combined comparative genomics with re-analysis of 97 ancient and modern dental calculus metagenomic datasets. Species-level relationships were assessed using average nucleotide identity, digital DNA-DNA hybridization, and 16S rRNA phylogeny. Metagenomic associations were examined using Kraken2-based taxonomic profiling, with Methanobrevibacter sp. YE315 as a proxy because M. massiliense was absent from the classifier database, and direct competitive read mapping to M. massiliense. Associations with P. piscolens were evaluated using Spearman correlation and negative binomial regression.

RESULTS: Comparative genomics supported TS-2 and M. massiliense as the same species-level taxon, with > 95% average nucleotide identity and > 90% digital DNA-DNA hybridization. In metagenomic analyses, the YE315 proxy was positively associated with P. piscolens in Kraken2 Spearman analysis (ρ = 0.3506, q = 0.0026), and mapped M. massiliense reproduced this pattern (ρ = 0.2939, q = 0.0153). Negative binomial models showed concordant but weaker support, whereas the signal for M. oralis was less consistent.

CONCLUSION: These results identify M. massiliense as the cultivated representative of TS-2 and support an ancient, recurrent association between M. massiliense and P. piscolens in dental calculus.},
}

@article {pmid42119293,
year = {2026},
author = {Li, H and Xu, Y and Lin, T and Hu, C and Yang, Z and Su, H},
title = {Overwintering waterbirds are important reservoirs for the spread of antibiotic resistance genes (ARGs): Shared patterns at the waterbird-environment interface and the risk of horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142298},
doi = {10.1016/j.jhazmat.2026.142298},
pmid = {42119293},
issn = {1873-3336},
abstract = {The global spread of antibiotic resistance genes (ARGs) has become a critical challenge to public health. Long-distance migratory waterbirds are recognized as important biological vectors in the transregional spread of ARGs. However, the sharing patterns of ARGs and the horizontal transfer risks between these birds and their habitats during the wintering period remain poorly understood. This limits a comprehensive understanding of their role in ARG transmission. This study investigated a typical wintering wetland in southwestern China along the East Asian-Australasian Flyway, using metagenomic approaches to systematically characterize the distribution patterns, sharing profiles, and horizontal transfer risks of ARGs in the guts of overwintering waterbirds and their associated aquatic and terrestrial habitats. The results show that multidrug resistance genes are the predominant type of resistance observed both in the guts of overwintering waterbirds and in their habitats. Extensive sharing of ARGs occurs between the guts of overwintering waterbirds and their habitats, with approximately 50% of the 1250 identified ARG subtypes shared by both. We detected 55 high-risk ARG subtypes belonging to 10 resistance categories. Among these, β-lactam resistance genes (e.g., blaNDM-5 and blaCTX-M-15) were the predominant types. In addition, the co-localization of ARGs with mobile genetic elements (MGEs) (e.g., transposons and plasmids) suggests that the gut of waterbirds and aquatic environments may represent potential hotspots for horizontal transfer of ARGs. This study highlights the high connectivity of ARGs between overwintering waterbirds and their habitats, offering important insights into ecological and public health risks related to ARG spread.},
}