@article {pmid41856866,
year = {2026},
author = {Jelen, BI and Baker, BJ},
title = {Mapping environmental microbiomes across an entire country.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.02.013},
pmid = {41856866},
issn = {1878-4380},
abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.},
}

@article {pmid41857415,
year = {2026},
author = {},
title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41857415},
issn = {2058-5276},
}

@article {pmid41857851,
year = {2026},
author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X},
title = {Respiratory syndromic disease study in Shanghai community population.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e103001},
doi = {10.1136/bmjopen-2025-103001},
pmid = {41857851},
issn = {2044-6055},
mesh = {Humans ; China/epidemiology ; Male ; Female ; *Respiratory Tract Infections/epidemiology/microbiology ; Adult ; Prospective Studies ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Child, Preschool ; Incidence ; Coinfection/epidemiology ; Urban Population ; Seasons ; },
abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.

PARTICIPANTS: The study enrolled 15 199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency ≥6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.

FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15 199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (≥3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.

FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.},
}

Humans
China/epidemiology
Male
Female
*Respiratory Tract Infections/epidemiology/microbiology
Adult
Prospective Studies
Middle Aged
Adolescent
Aged
Child
Young Adult
Child, Preschool
Incidence
Coinfection/epidemiology
Urban Population
Seasons

@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

Humans
*Gastrointestinal Microbiome/immunology
Adult
Young Adult
*Brassica
Quality of Life
*Fermented Foods
Adolescent
Randomized Controlled Trials as Topic
*Conjunctivitis, Allergic/immunology/diet therapy
*Rhinitis, Allergic/immunology/diet therapy
Female
Male
Biomarkers

@article {pmid41858204,
year = {2026},
author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W},
title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71089},
pmid = {41858204},
issn = {1469-8137},
support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; },
abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.},
}

@article {pmid41858247,
year = {2026},
author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU},
title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70286},
doi = {10.1111/1462-2920.70286},
pmid = {41858247},
issn = {1462-2920},
support = {101118631/ERC_/European Research Council/International ; },
mesh = {*Carbon Dioxide/metabolism/analysis ; *Archaea/genetics/metabolism/chemistry ; Germany ; *Groundwater/microbiology ; *Lipids/chemistry ; *Ethers/chemistry ; Metagenome ; *Glyceryl Ethers/chemistry ; },
abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.},
}

*Carbon Dioxide/metabolism/analysis
*Archaea/genetics/metabolism/chemistry
Germany
*Groundwater/microbiology
*Lipids/chemistry
*Ethers/chemistry
Metagenome
*Glyceryl Ethers/chemistry

@article {pmid41858251,
year = {2026},
author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L},
title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70131},
doi = {10.1111/1755-0998.70131},
pmid = {41858251},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; },
abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/classification/genetics
*DNA, Environmental/genetics
Quebec
Ecosystem
Fresh Water
Rivers
*Biological Monitoring/methods
Biodiversity
*Environmental Monitoring/methods
*Metagenomics/methods
*Biota

@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
doi = {10.1111/1755-0998.70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}

*Metagenomics/methods
*Diatoms/genetics/classification
Phylogeny
*Computational Biology/methods
*DNA, Environmental/genetics
*Eukaryota/genetics/classification
Metagenome
*Biodiversity
Czech Republic
Fresh Water/microbiology

@article {pmid41858380,
year = {2026},
author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V},
title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf315},
pmid = {41858380},
issn = {2635-0041},
abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.

RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.

The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.},
}

@article {pmid41858392,
year = {2026},
author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L},
title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.},
journal = {World journal of emergency medicine},
volume = {17},
number = {2},
pages = {199-201},
pmid = {41858392},
issn = {1920-8642},
}

@article {pmid41858535,
year = {2026},
author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H},
title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1659863},
pmid = {41858535},
issn = {2297-1769},
abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.

METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.

RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.

DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.},
}

@article {pmid41858674,
year = {2026},
author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z},
title = {Microbiome and plant relationship: a symbiosis against phytopathogens.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1722279},
pmid = {41858674},
issn = {1664-462X},
abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.},
}

@article {pmid41859061,
year = {2026},
author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L},
title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {565781},
pmid = {41859061},
issn = {1178-6973},
abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.},
}

@article {pmid41859064,
year = {2026},
author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y},
title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {556094},
pmid = {41859064},
issn = {1178-6973},
abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.},
}

@article {pmid41859067,
year = {2026},
author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y},
title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {562973},
pmid = {41859067},
issn = {1178-6973},
abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.

METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.

RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd±) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.

CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.},
}

@article {pmid41859237,
year = {2026},
author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H},
title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag011},
pmid = {41859237},
issn = {2730-6151},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.},
}

@article {pmid41859321,
year = {2026},
author = {Salama, RA and Abdel Kader, RG and Wadid, NA},
title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.},
journal = {Infection prevention in practice},
volume = {8},
number = {2},
pages = {100522},
pmid = {41859321},
issn = {2590-0889},
abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.},
}

@article {pmid41859442,
year = {2026},
author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C},
title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1756020},
pmid = {41859442},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.

METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.

RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.

DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.},
}

@article {pmid41859445,
year = {2026},
author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W},
title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783810},
pmid = {41859445},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.},
}

@article {pmid41859451,
year = {2026},
author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L},
title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755652},
pmid = {41859451},
issn = {1664-302X},
abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.},
}

@article {pmid41860433,
year = {2026},
author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A},
title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag029},
pmid = {41860433},
issn = {1574-6941},
abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesising that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularised regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.},
}

@article {pmid41860453,
year = {2026},
author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A},
title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09604},
pmid = {41860453},
issn = {1520-5851},
abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.},
}

@article {pmid41860568,
year = {2026},
author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J},
title = {Klebsiella Enrichment Is Associated with Disease Severity in Ulcerative Colitis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag079},
pmid = {41860568},
issn = {1365-2672},
abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.

METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.

RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.

CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.},
}

@article {pmid41860897,
year = {2026},
author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S},
title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {3},
pages = {e0014118},
doi = {10.1371/journal.pntd.0014118},
pmid = {41860897},
issn = {1935-2735},
abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.},
}

@article {pmid41861238,
year = {2026},
author = {Yao, ML and Dai, Y and Zhang, W},
title = {Natural Products from the Oral Microbiome.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-050248},
pmid = {41861238},
issn = {1545-4509},
abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.},
}

@article {pmid41861543,
year = {2026},
author = {Mohapatra, RK and Choi, Y},
title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129342},
doi = {10.1016/j.jenvman.2026.129342},
pmid = {41861543},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.},
}

@article {pmid41861844,
year = {2026},
author = {Tam, KK and Suster, CJE and Fong, W and Golubchik, T and Sivalingam, V and Jeoffreys, N and Tay, E and Ko, D and Wehrhahn, MC and Ginn, AN and Robson, J and Gardner, I and Papanicolas, LE and Kennedy, K and Graham, M and Tran, T and Speers, D and Cooley, L and Baird, RW and Meumann, EM and Harbidge, J and Campbell, S and Basile, K and Chen, SC and Sintchenko, V and Kok, J and Rockett, RJ},
title = {Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag163},
pmid = {41861844},
issn = {1537-6613},
abstract = {BACKGROUND: The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among children under 15. While MRMP remains low in Europe, North America, and Australia (<5%), limited routine testing and surveillance restricts understanding of resistance dynamics. As macrolides are first-line therapy in many health settings, MRMP surveillance is essential for guiding empirical treatment and stewardship.

METHODS: We applied a novel capture-based targeted metagenomic sequencing (tNGS) to PCR-positive MP specimens (n=356) from across Australia. This approach enabled whole-genome recovery and MRMP detection directly from clinical specimens, without culture. MRMP detections were benchmarked against RT-PCR and clinical data were analysed to assess associations between resistance and healthcare utilisation.

RESULTS: This is the first genomics-informed national study of MP in Australia. We recovered 124 high-quality genomes, revealing a genetically diverse population with co-circulation of P1 Type 1 (69%) and Type 2 (31%). MRMP was identified in 13% of genomes, all belonging to clades prior to 2024 had only been reported in Asia (ST3 and ST14). MRMP cases were geographically widespread, suggesting importation and local transmission. Unlike reports from China, macrolide-susceptible clades (ST3, ST7, ST17 and ST20) predominated (87%) and were associated to significant lower healthcare utilisation compared to MRMP cases.

CONCLUSION: Our findings demonstrate the utility of tNGS for genomic epidemiology and highlight the need for MRMP surveillance. Although macrolides remain effective in Australia, emerging MRMP strains require close monitoring to inform treatment guidelines and antimicrobial stewardship.},
}

@article {pmid41861946,
year = {2026},
author = {Wang, ST and Li, L and Yang, Q and Zhang, GF},
title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124314},
doi = {10.1016/j.envres.2026.124314},
pmid = {41861946},
issn = {1096-0953},
abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.},
}

@article {pmid41861947,
year = {2026},
author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S},
title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124311},
doi = {10.1016/j.envres.2026.124311},
pmid = {41861947},
issn = {1096-0953},
abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71±102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34±4.27 nmol/(kg·h)). On average, both N2ODen (115.34±143.60 nmol/(kg·h)) and N2ONif (5.29±4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56±62.52 and 3.88±4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.},
}

@article {pmid41418935,
year = {2026},
author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y},
title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {35-47},
doi = {10.1016/j.virs.2025.12.009},
pmid = {41418935},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; },
abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.},
}

Animals
China/epidemiology
*Shrews/virology
*Rodentia/virology
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Virome
Rats
Genetic Variation
Evolution, Molecular
Metagenomics
Gene Expression Profiling

@article {pmid41850962,
year = {2026},
author = {Zhao, Y and Zheng, J and Liu, Q},
title = {The diversity of emerging tick-borne viruses globally.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.03.001},
pmid = {41850962},
issn = {1471-5007},
abstract = {Zhang et al. provide the first global synthesis of 230 emerging tick-borne viruses, introducing a genomic model that predicts zoonotic risk. Their approach identifies 25 very-high-risk viruses and clinically validates three novel human pathogens, shifting the paradigm from reactive discovery to proactive risk assessment for global health security.},
}

@article {pmid41851124,
year = {2026},
author = {Luzmore, A and Grauer, J and Barber, D and Lau, P and Jorgensen, G and Jain, S and Perron, GG},
title = {Seasonal frost improves probiotic and nutrient availability in fermented vegetables.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00776-w},
pmid = {41851124},
issn = {2396-8370},
abstract = {Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K2), cobalamin (B12), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K1 in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.},
}

@article {pmid41851530,
year = {2026},
author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E},
title = {Advances and opportunities in measuring dietary intake: from omics to AI.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41851530},
issn = {2522-5812},
abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.},
}

@article {pmid41851880,
year = {2026},
author = {Sharma, AA and Martinou, AF and Cadar, D and Omirou, M and Neira, M and Christophides, GK},
title = {Integrated vector and arbovirus surveillance in Cyprus: first reports of Usutu virus and Culex pipiens bioform diversity highlight potential for zoonotic arbovirus transmission.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07350-z},
pmid = {41851880},
issn = {1756-3305},
support = {856612//Horizon 2020/ ; },
abstract = {BACKGROUND: Anthropogenic pressures, including urbanisation, globalisation and climate change, have facilitated an increased risk for emergence or re-emergence of mosquito-borne diseases into regions such as the Eastern Mediterranean and Middle East. Cyprus is a major stop-over site for migratory birds and has previously experienced outbreaks of West Nile virus (WNV). The island has native mosquito vector populations; however, it has also seen the recent establishment of invasive Aedes albopictus and Ae. aegypti mosquitoes. Given the dynamic climatic conditions and the shifting ecological and epidemiological landscapes in the region, the need for routine vector and pathogen surveillance has never been more critical.

METHODS: Herein, we present the results from localised adult mosquito surveillance that were conducted in two cities of Cyprus between 2019 and 2022. Mosquito taxa were identified through morphological analysis, and molecular techniques were used to further characterise the Culex pipiens bioforms. Engorged mosquito midguts were analysed to determine host blood meals. Metagenomic next-generation sequencing was employed to screen mosquito pools for arboviruses.

RESULTS: Our results provide the first report of Usutu virus in Cx. pipiens mosquitoes in Cyprus. Blood meal analysis identified multiple vertebrate hosts, including Cetti's warbler, a bird species previously reported to be seropositive for WNV on the island. Additionally, we report the presence of both Cx. pipiens pipiens and Cx. pipiens molestus, an ornithophilic and a mammophilic bioform, respectively, as well as their hybrids.

CONCLUSIONS: Our findings highlight the urgent need for enhanced mosquito surveillance strategies where mosquito populations will be regularly screened for pathogens to mitigate emerging risks of arbovirus transmission in Cyprus.},
}

@article {pmid41851941,
year = {2026},
author = {Shrestha, E and Katuwal, N and Sitaula, RK and Gurung, H and Shrestha, A and Karki, P and Shrestha, R},
title = {Identification of the Causative Pathogen in the 2023 Conjunctivitis Outbreak of Nepal Using Unbiased Metagenomic Next Generation Sequencing.},
journal = {Journal of Nepal Health Research Council},
volume = {23},
number = {3},
pages = {527-532},
doi = {10.33314/jnhrc.v23i03.4749},
pmid = {41851941},
issn = {1999-6217},
mesh = {Humans ; Nepal/epidemiology ; *Disease Outbreaks ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Metagenomics/methods ; *Conjunctivitis/epidemiology/virology ; Adult ; Child, Preschool ; *Enterovirus C, Human/isolation & purification/genetics ; Adolescent ; Young Adult ; Middle Aged ; Infant ; },
abstract = {BACKGROUND: In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. Most cases exhibited acute haemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This case series from Himalaya Eye Hospital in Pokhara details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak.

METHODS: To understand the causative agents, conjunctival swabs from patients were subjected to unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital Results: This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak.

CONCLUSIONS: This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.},
}

Humans
Nepal/epidemiology
*Disease Outbreaks
Female
*High-Throughput Nucleotide Sequencing
Male
Child
*Metagenomics/methods
*Conjunctivitis/epidemiology/virology
Adult
Child, Preschool
*Enterovirus C, Human/isolation & purification/genetics
Adolescent
Young Adult
Middle Aged
Infant

@article {pmid41852102,
year = {2026},
author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X},
title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70268},
doi = {10.1111/1462-2920.70268},
pmid = {41852102},
issn = {1462-2920},
support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; },
abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.},
}

*Soil Microbiology
*Forests
*Symbiosis
*Soil/chemistry
*Fungi/genetics/classification/physiology
China
Phosphorus/metabolism
Carbon/metabolism
Nitrogen/metabolism
Biodiversity
Bacteria/genetics/classification
Ecosystem

@article {pmid41852114,
year = {2026},
author = {Kaneko, Y and Hino, T and Taminishi, S and Matoba, Y and Motooka, D and Hoshino, A and Matoba, S},
title = {Inhibition of N-Terminal Acetyltransferase C Mitigates Endoplasmic Reticulum Stress-Mediated Muscle Atrophy in Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {2},
pages = {e70249},
doi = {10.1002/jcsm.70249},
pmid = {41852114},
issn = {2190-6009},
support = {22H03071//JSPS Grant-in-Aid Scientific Research/ ; 25K02651//JSPS Grant-in-Aid Scientific Research/ ; //Nakatomi Foundation/ ; },
mesh = {Animals ; *Cachexia/etiology/pathology ; *Endoplasmic Reticulum Stress ; *Muscular Atrophy/etiology/pathology/metabolism ; Mice ; Male ; *Neoplasms/complications ; Humans ; Unfolded Protein Response ; },
abstract = {BACKGROUND: Cancer cachexia is a complex syndrome marked by weight loss and muscle wasting, significantly impacting patient quality of life and survival. Mechanistically, it is characterized by suppressed protein synthesis and enhanced muscle catabolism, with the role of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) becoming increasingly evident. This study aimed to explore ER stress-tolerant factors in muscle wasting and evaluate their potential to prevent muscle loss in cancer cachexia.

METHODS: A genome-wide CRISPR screening was conducted in the context of ER stress-mediated growth inhibition of C2C12 myoblasts. The candidate genes resistant to ER stress were further evaluated in C2C12 myotubes treated with conditioned medium of Lewis lung adenocarcinoma (LLC) cells. Twelve-week-old male mice were administered LLC cells and shRNA against Naa35 via adeno-associated virus. Four weeks later, tibialis anterior (TA) muscles were analysed for muscle mass, grip strength and molecular changes with quantitative polymerase chain reaction, western blotting and histological analysis.

RESULTS: CRISPR screening identified Naa35, Naa38 and Naa30, all three components of N-terminal acetyltransferase C, as key molecules for resistance to ER stress. The atrophic muscles of mice bearing LLC demonstrated an elevation of UPR, as well as 1.64-fold upregulation of Naa35 protein (p = 0.0072). Among the three branches of the UPR, an ATF6 inhibitor, AEBSF, abolished upregulation of Naa35, Naa38 and Naa30, and an ATF6 activator, AA147, induced Naa35 expression in a dose-dependent manner (p < 0.001). In cells treated with LLC conditioned medium, Naa35 knockdown reduced the amount of cathepsin K (CTSK) protein, which subsequently resulted in the CTSK-mediated proteolysis of insulin receptor substrate 1. In LLC-bearing mice, Naa35 knockdown led to a 65.4% reduction in CTSK protein expression (p < 0.001) and preservation of the phosphorylation levels of protein kinase B (p < 0.0324) and anabolic-related S6 kinase (p < 0.0375). Concurrently, the expression of catabolism-related genes was repressed (MuRF1, p < 0.0015; MAFbx1, p < 0.0265). These alterations were associated with the restoration of TA muscle mass (2.52 ± 0.19 vs. 3.72 ± 0.45 mg/g, p = 0.0004), fibre area (1741 ± 992 vs. 2099 ± 1264 mm[2], p < 0.0001), grip strength in all four limbs (0.0328 ± 0.0076 vs. 0.0506 ± 0.0130 N/g, p = 0.0295) and wire mesh hanging time (496 ± 331 vs. 1038 ± 370 s, p = 0.0406).

CONCLUSIONS: Inhibition of N-terminal acetyltransferase C prevents ER stress-induced muscle wasting via the downregulation of CTSK and subsequent activation of the anabolic pathway. This suggests that N-terminal acetyltransferase C is a potential therapeutic target for combating muscle wasting in cancer cachexia.},
}

Animals
*Cachexia/etiology/pathology
*Endoplasmic Reticulum Stress
*Muscular Atrophy/etiology/pathology/metabolism
Mice
Male
*Neoplasms/complications
Humans
Unfolded Protein Response

@article {pmid41852383,
year = {2025},
author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M},
title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1672438},
pmid = {41852383},
issn = {2813-4338},
abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.},
}

@article {pmid41852393,
year = {2025},
author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B},
title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1592023},
pmid = {41852393},
issn = {2813-4338},
abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.

METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.

RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (α-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (β-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (α-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.

DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.},
}

@article {pmid41852395,
year = {2025},
author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C},
title = {Interplay between host genetics and gut microbiome composition in the Japanese population.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1635907},
pmid = {41852395},
issn = {2813-4338},
abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.

METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.

RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10[-8]). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.

CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.},
}

@article {pmid41852396,
year = {2025},
author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K},
title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1688681},
pmid = {41852396},
issn = {2813-4338},
abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.

RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[™] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[®] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.

CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.},
}

@article {pmid41852403,
year = {2025},
author = {Helal, M and Bari, VK},
title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1549166},
pmid = {41852403},
issn = {2813-4338},
abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.},
}

@article {pmid41852404,
year = {2025},
author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y},
title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1531991},
pmid = {41852404},
issn = {2813-4338},
abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.

METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.

RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.

CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.},
}

@article {pmid41852413,
year = {2025},
author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH},
title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1707779},
pmid = {41852413},
issn = {2813-4338},
abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.},
}

@article {pmid41852418,
year = {2025},
author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S},
title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1619859},
pmid = {41852418},
issn = {2813-4338},
abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.},
}

@article {pmid41852432,
year = {2025},
author = {Mhuireach, GÁ and Collins, S and Dietz, L and Horve, PF and Laguerre, A and Northcutt, D and Stenson, J and Wymelenberg, KVD and Gall, E and Fretz, M},
title = {Effects of wetting events on mass timber surface microbial communities and VOC emissions: implications for building operation and occupant well-being.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1395519},
pmid = {41852432},
issn = {2813-4338},
abstract = {INTRODUCTION: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.

METHODS: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.

RESULTS: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.},
}

@article {pmid41852435,
year = {2025},
author = {Trubl, G and Malard, L and Rahlff, J},
title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1604002},
doi = {10.3389/frmbi.2025.1604002},
pmid = {41852435},
issn = {2813-4338},
}

@article {pmid41852443,
year = {2025},
author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F},
title = {Position statement of the Microbiota International Clinical Society.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1657750},
pmid = {41852443},
issn = {2813-4338},
}

@article {pmid41852664,
year = {2026},
author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H},
title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748638},
pmid = {41852664},
issn = {2235-2988},
mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.},
}

Humans
Male
*Urinary Tract Infections/microbiology
*Renal Insufficiency, Chronic/complications/microbiology
Middle Aged
*Microbiota
*Drug Resistance, Bacterial
RNA, Ribosomal, 16S/genetics
Aged
*Urine/microbiology
Metagenomics
*Bacteria/genetics/drug effects/classification/isolation & purification
Adult
Microscopy, Electron, Transmission
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/chemistry/genetics
*Extracellular Vesicles/ultrastructure
Anti-Bacterial Agents/pharmacology

@article {pmid41852665,
year = {2026},
author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L},
title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1728182},
pmid = {41852665},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; },
abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.

METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.

RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.

CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.},
}

Humans
*Microbiota
Dysbiosis/microbiology
*Urologic Diseases/microbiology/diagnosis
*Urinary Tract/microbiology
*Urine/microbiology
Prostatic Neoplasms/microbiology

@article {pmid41852689,
year = {2026},
author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV},
title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1742803},
pmid = {41852689},
issn = {2813-4338},
abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.},
}

@article {pmid41852814,
year = {2022},
author = {Jagadeeshwari, U and Sasikala, C and Rai, A and Indu, B and Ipsita, S and Ramana, CV},
title = {Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis.},
journal = {Frontiers in microbiomes},
volume = {1},
number = {},
pages = {1020341},
pmid = {41852814},
issn = {2813-4338},
abstract = {INTRODUCTION: Host-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.

METHODS: We report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.

RESULTS AND DISCUSSION: The phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated 'Candidatus' superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with 'Candidatus Heimdallarchaeota' were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb's pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.},
}

@article {pmid41852815,
year = {2022},
author = {van Belkum, A and Lisotto, P and Pirovano, W and Mongiat, S and Zorgani, A and Gempeler, M and Bongoni, R and Klaassens, E},
title = {Being friendly to the skin microbiome: Experimental assessment.},
journal = {Frontiers in microbiomes},
volume = {1},
number = {},
pages = {1077151},
pmid = {41852815},
issn = {2813-4338},
abstract = {Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically "microbiome friendly" while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.},
}

@article {pmid41852816,
year = {2022},
author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R},
title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.},
journal = {Frontiers in microbiomes},
volume = {1},
number = {},
pages = {1097124},
pmid = {41852816},
issn = {2813-4338},
abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.},
}

@article {pmid41852852,
year = {2026},
author = {Gusareva, ES and Vettath, VK and Gaultier, NE and Sadovoy, AV and Dacanay, JGA and Schuster, SC},
title = {Dermatophagoides pteronyssinus in ambient air bioaerosols.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {5},
number = {3},
pages = {100667},
pmid = {41852852},
issn = {2772-8293},
abstract = {BACKGROUND: House dust mite (HDM) sensitization is a leading cause of allergic rhinitis and asthma worldwide, with Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Blomia tropicalis being the primary allergenic species typically associated with indoor environments. Even effective multicomponent interventions creating an HDM-free indoor environment are often insufficient to prevent allergy, as HDM exposure may also occur outdoors.

OBJECTIVE: To assess the potential for outdoor HDM exposure, we applied air biomass sequencing and metagenomic techniques to detect HDM DNA in both indoor and outdoor bioaerosols, offering an alternative to conventional dust sampling methods.

METHODS: We used 2 data sets in this study: (1) a global data set comprising 1,171 outdoor air samples collected across 33 countries in open air environments and (2) a data set of indoor (n = 161) and outdoor (n = 156) air samples collected across 156 apartments from 106 locations in Singapore. All air samples were collected by drawing 24,000 to 36,000 L of air using SASS3100 air samplers; all samples were processed identically. Species-level taxonomic classification was performed using Kaiju software aligned to the National Center for Biotechnology Information nonredundant database, with a minimum threshold of 40 reads per taxon.

RESULTS: Analysis of 1,171 global outdoor air samples revealed D pteronyssinus as the most prevalent HDM species; it was detected in 208 samples, with abundance increasing from temperate toward equatorial regions. In Singaporean households, D pteronyssinus was found in 58.4% of indoor samples and 21.2% of nearby outdoor samples, with high median DNA read counts outdoors suggesting that exposure to HDM is not limited to domestic environments. B tropicalis and D farinae were also detected in Singapore, albeit at lower frequencies.

CONCLUSION: Our findings highlight the need to expand environmental allergen surveillance beyond household dust to include ambient and outdoor air, particularly in tropical climates.},
}

@article {pmid41853108,
year = {2026},
author = {Khan, A},
title = {Disseminated Mycobacterium intracellulare subsp. chimaera infection, undiagnosed for years, highlights the enduring clinical utility of "old school" microbiological testing and a robust differential.},
journal = {ASM case reports},
volume = {2},
number = {2},
pages = {},
pmid = {41853108},
issn = {2996-2684},
abstract = {Disseminated Mycobacterium intracellulare subsp. chimaera (MC) infections are rare, slow-progressing, and easily overlooked, particularly when a patient's history of prior cardiac surgery is not incorporated into the diagnostic evaluation. In a recent ASM Case Reports article (1:e00003-25, 2025, https://doi.org/10.1128/asmcr.00003-25), Ladines-Lim et al. describe a disseminated MC infection in a patient with prior aortic and mitral valve replacement that remained undiagnosed for over 4 years. Conventional microbiological testing was not pursued early in the course of illness because the history of cardiopulmonary bypass was not linked with the constellation of unexplained symptoms. This case urges clinicians to remain vigilant and suspect MC in patients with prior open-chest cardiac surgery who present with gradually worsening, systemic symptoms. Since 2013, global outbreaks of delayed-onset MC infections have been traced to contaminated heater cooler devices, yet many centers continue to face barriers to replacing or monitoring such equipment. A delayed diagnosis in this case was eventually established by cell-free metagenomic next-generation sequencing (cfmNGS). However, the result was not acted upon until weeks later, after central nervous system involvement. A more timely, cost-effective diagnosis might have been achieved using traditional, widely available, culture-based testing guided by a robust exposure-driven differential. Clinicians should suspect MC in patients with prior cardiac surgery-even years earlier-who develop unexplained, progressive systemic symptoms. Early suspicion and appropriate testing are critical to improved outcomes. This case shows that next-generation sequencing assays are only as useful as the clinical reasoning guiding their use. Traditional microbiological testing-when leveraged early and thoughtfully-remains an accessible cornerstone of diagnosing complex MC infections.},
}

@article {pmid41853337,
year = {2023},
author = {Peter, H and Michoud, G and Busi, SB and Battin, TJ},
title = {The role of phages for microdiverse bacterial communities in proglacial stream biofilms.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1279550},
pmid = {41853337},
issn = {2813-4338},
abstract = {Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.},
}

@article {pmid41853339,
year = {2023},
author = {Wong, MT and Nesbø, CL and Wang, W and Couturier, M and Lombard, V and Lapebie, P and Terrapon, N and Henrissat, B and Edwards, EA and Master, ER},
title = {Taxonomic composition and carbohydrate-active enzyme content in microbial enrichments from pulp mill anaerobic granules after cultivation on lignocellulosic substrates.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1094865},
pmid = {41853339},
issn = {2813-4338},
abstract = {Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (> 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.},
}

@article {pmid41853340,
year = {2023},
author = {Yang, Q and Wang, J and Zhang, D and Feng, H and Bozorov, TA and Yang, H and Zhang, D},
title = {Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1248384},
pmid = {41853340},
issn = {2813-4338},
abstract = {Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis, in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.},
}

@article {pmid41853343,
year = {2023},
author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y},
title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1329925},
pmid = {41853343},
issn = {2813-4338},
abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.},
}

@article {pmid41853350,
year = {2023},
author = {Oliveira, RS and Pinto, OHB and Quirino, BF and de Freitas, MAM and Thompson, FL and Thompson, C and Kruger, RH},
title = {Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1206961},
pmid = {41853350},
issn = {2813-4338},
abstract = {The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge's microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group's abundance in GARS sponges. The workflow consisted of MAG's quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host's survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.},
}

@article {pmid41853380,
year = {2023},
author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN},
title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1067019},
pmid = {41853380},
issn = {2813-4338},
abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.},
}

@article {pmid41853383,
year = {2023},
author = {Ramirez Garcia, A and Greppi, A and Constancias, F and Ruscheweyh, HJ and Gasser, J and Hurley, K and Sturla, SJ and Schwab, C and Lacroix, C},
title = {Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1194516},
pmid = {41853383},
issn = {2813-4338},
abstract = {INTRODUCTION: Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function.

METHODS: In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase (gdh)-harboring taxa, the proportion of resident A. hallii, and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10[6] cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized.

RESULTS AND DISCUSSION: Six microbiota were assigned to Bacteroides, nine to Prevotella, and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10[10] bacterial cells ranged between 1.32 × 10[8] and 1.15 × 10[9]. Eighteen out of the 20 donors were dominated by A. hallii, representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low-A. hallii-abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii, for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.},
}

@article {pmid41853385,
year = {2023},
author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P},
title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1147082},
pmid = {41853385},
issn = {2813-4338},
abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.

OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).

METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.

RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.

CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.},
}

@article {pmid41853387,
year = {2023},
author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC},
title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1199766},
pmid = {41853387},
issn = {2813-4338},
abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.},
}

@article {pmid41853501,
year = {2024},
author = {Faber, Q and Davis, C and Christner, B},
title = {Metagenomic inference of microbial community composition and function in the weathering crust aquifer of a temperate glacier.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1488744},
pmid = {41853501},
issn = {2813-4338},
abstract = {Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier's ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems.},
}

@article {pmid41853503,
year = {2024},
author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T},
title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1451735},
pmid = {41853503},
issn = {2813-4338},
abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.},
}

@article {pmid41853504,
year = {2024},
author = {Muwonge, A and Gerber, PF and Wee, BA and Thomson, J and Wang, J and Halbur, PG and Opriessnig, T},
title = {Exploring the utility of bioaerosol metagenomics compared to PCRs for swine pathogen surveillance.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1439108},
pmid = {41853504},
issn = {2813-4338},
abstract = {INTRODUCTION: Pathogen introduction and transmission at the farm, regional, or national level are associated with reduced animal welfare and negative impacts on herd economics. Ongoing infectious disease surveillance, active or passive, is therefore of high importance. For optimal resolution, each pig is sampled individually, for example by collecting blood or nasal swabs. In recent years, oral fluids have become very useful for population surveillance at the pen level. Another alternative is sampling the air to capture pathogens circulating across the entire barn via bioaerosols.

OBJECTIVE: This study aimed to examine the potential utility of bioaerosol metagenomics for pathogen detection on pig farms.

METHODS: Bioaerosols via automated air sampler, and oral fluid via pen-based ropes, were collected from each of two Scottish indoor pig farms. All samples were subjected to conventional routine bacterial isolation. Total genomic nucleic acids were extracted for PCR screening for three pig DNA viruses, three bacterial Mycoplasma species and an RNA virus. Illumina shotgun metagenomic sequencing was also conducted.

RESULTS: Oral fluids contained more DNA compared to bioaerosol samples. DNA integrity exhibited limited impact on PCR or sequence yield. While Streptococcus suis could be cultured from a single oral fluid sample, reads mapped to S. suis were detectable in all metagenomic samples. Other bacterial pig pathogens, including Mycoplasma hyorhinis, M. hyopneumoniae and M. hyosynoviae, were detected in oral fluid and aerosols by PCR and metagenomics. One of the two farms was PRRSV positive, and the virus was detectable via PCR in oral fluids but not in bioaerosols. Antimicrobial resistance (AMR) gene profiles had less variation between bioaerosols and oral fluids. Some identified AMR genes had strikingly similar abundance overall.

CONCLUSION: Overall, these findings indicate that there is potential utility of bioaerosol metagenomics for pathogen surveillance on pig farms; however, more research is needed for technical and cost optimization to allow for routine pathogen detection on livestock farms.},
}

@article {pmid41853506,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1484878},
doi = {10.3389/frmbi.2024.1484878},
pmid = {41853506},
issn = {2813-4338},
abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].},
}

@article {pmid41853507,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1359580},
pmid = {41853507},
issn = {2813-4338},
abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.},
}

@article {pmid41853508,
year = {2024},
author = {Molotzu, MR and Cabras, PA and Di Marcantonio, L and Atzeni, R and Macciotta, NPP and Canu, A},
title = {Metagenomic analysis of goat feces from Ogliastra (Sardinia, Italy).},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1474497},
pmid = {41853508},
issn = {2813-4338},
abstract = {With its constitutive and functional characteristics, the intestinal microbiota plays a crucial role in the health condition of the animals. Variations in the composition and gene expression of the intestinal microbiota are associated with the risk of the onset of various pathologies of the gastrointestinal tract and chronic inflammatory intestinal diseases. The objectives of this study were to evaluate the variability in the composition of the intestinal microbiota of goats of different breeds (Sarda, Maltese, and Alpine) farmed in different flocks of the region of Ogliastra (Sardegna, Italy) and to assess whether the type of feeding (natural pasture grazing-based versus intensive) could affect the intestinal bacterial composition. We also evaluated possible differences in the composition of the intestinal microbiota between healthy and Caprine arthritis encephalitis (CAE)-affected goats. The economic damage caused by this pathology is due to the reduction in milk production, with infected animals having greater susceptibility to contract diseases. The results of our study highlighted a statistically significant difference (P = 0.001-0.005) in the intestinal bacterial composition between the intensively managed flock and the other natural pasture-based flock.g In particular, a significantly greater abundance of Acidoaminococcaceae in the intensive flock was obgserved. Furthermore, a significantly greater abundance of Prevotellaceae was found in two localities in which, out of a total of 29 animals, only four tested negative for CAE. From these data, we deduced that the presence of Prevotellaceae can be an indication of the disease. This difference could be attributed to the farming system, the Cardedu farm being the only intensive one, and to the geographical distance of this location from the other sampling sites. Therefore, the results of the present study suggest that extensive or intensive farm management may affect the intestinal microbiota of goats.},
}

@article {pmid41853526,
year = {2024},
author = {Liu, S and Zhao, J and Feng, WL and Zhang, ZJ and Gu, YF and Wang, YP},
title = {Microbial community succession of cow manure and tobacco straw composting.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1301156},
pmid = {41853526},
issn = {2813-4338},
abstract = {Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.},
}

@article {pmid41853529,
year = {2024},
author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM},
title = {Phage communities in household-related biofilms correlate with bacterial hosts.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1396560},
pmid = {41853529},
issn = {2813-4338},
abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.},
}

@article {pmid41853533,
year = {2024},
author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z},
title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1384703},
pmid = {41853533},
issn = {2813-4338},
abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.

METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.

RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.

DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.},
}

@article {pmid41853535,
year = {2024},
author = {Alian, OM and Brazelton, WJ and Aquino, KA and Twing, KI and Pendleton, HL and Früh-Green, G and Lang, SQ and Schrenk, MO},
title = {Microbial community differentiation in vent chimneys of the Lost City Hydrothermal Field reflects habitat heterogeneity.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1401831},
pmid = {41853535},
issn = {2813-4338},
abstract = {Oceanic hydrothermal vent systems represent some of the oldest habitats on Earth and serve as analogs for extraterrestrial environments. The Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge is one such environment, and its large chimneys are unique in hosting actively venting hydrothermal fluids that are primarily controlled by serpentinization reactions in the subseafloor. Microbial communities within LCHF have been studied for insights into their functional adaptations to the warm, alkaline, and dissolved inorganic carbon-limited environment. Metagenomic and mineralogical data collected during a recent expedition to Lost City were analyzed to delineate associations between microbial populations and physical, chemical and biological characteristics of the chimneys. Bacterial 16S rRNA gene sequences show a high degree of putative microdiversity within the relatively dominant genera Desulfotomaculum, Sulfurovum, Thiomicrorhabdus, and Serpentinicella, which represent a large core of the overall LCHF vent bacterial community. This microdiversity relates to the compositional fraction of aragonite, brucite, and calcite minerals within chimney samples rather than just the composition of nearby vent fluids. Although many species are found in both chimneys and venting fluids, the overall microbial community structures in chimney biofilms remain distinct from the hydrothermal fluids that flow through them. Shotgun metagenomic analyses reveal differences among genes predicted to be involved in carbon, methane, nitrogen and sulfur cycling with respect to their correlations to the abundances of specific minerals. These data hint at microenvironmental complexity lost within standard bulk analyses. The findings of this study underscore the need to more closely examine microbe-mineral interactions in natural environments, critically informing not just population-level distributions, but also the functional underpinnings of these extremophile microbial communities.},
}

@article {pmid41853539,
year = {2024},
author = {Chandel, N and Gorremuchu, JP and Thakur, V},
title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1432646},
pmid = {41853539},
issn = {2813-4338},
abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.

METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.

RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.

DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.},
}

@article {pmid41853546,
year = {2024},
author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA},
title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1457537},
pmid = {41853546},
issn = {2813-4338},
abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.

METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.

RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.

CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.},
}

@article {pmid41853549,
year = {2024},
author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R},
title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1408203},
pmid = {41853549},
issn = {2813-4338},
abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.},
}

@article {pmid41853558,
year = {2024},
author = {Pannoni, SB and Holben, WE},
title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1274277},
pmid = {41853558},
issn = {2813-4338},
abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.},
}

@article {pmid41853664,
year = {2026},
author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Links, MG and Waldner, CL},
title = {Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.},
journal = {Veterinary and animal science},
volume = {32},
number = {},
pages = {100609},
pmid = {41853664},
issn = {2451-943X},
abstract = {Short nasal swabs (SNS) have potential advantages of lower costs, collection time and training of personnel than deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens. This study examined differences between DNPS and SNS in BRD-associated pathogens detected using a nanopore metagenomic sequencing protocol, optimized for respiratory RNA viruses, collected from 150 calves in six feedlot pens. Short nasal swabs yielded higher viral read counts and prevalence than DNPS for BCoV (mean reads 75 versus 17; OR = 21.4, P = 0.001) and IDV (mean reads: 560 versus 192; OR = 2.60, P = 0.02). Agreement varied among viruses: IDV (κ=0.57), BRSV (κ=0.43), and BCoV at both ≥1 read (κ=0.35) and ≥30 reads (κ=0.10). No BoHV-1 and BAdV3 were detected. Mannheimia haemolytica was detected (≥14 reads) more frequently in SNS than DNPS (mean reads: 169 versus 57; OR = 5.73, P = 0.001), as was Pasteurella multocida (≥ 1 read) (mean reads: 4.0 versus 1.2; OR = 2.02, P = 0.02). Mesomycoplasma dispar was less prevalent in SNS (mean reads: 5.2 versus 29; OR = 0.27, P = 0.001). Detection of Histophilus somni, Bibersteinia trehalosi, and Mycoplasmopsis bovis did not differ between swab types. Agreement for detection of M. haemolytica (≥14 reads) was moderate (κ = 0.46, P = 0.001). For all other bacteria examined in this analysis, kappa values were very low. Short nasal swabs were a sensitive and practical alternative for BRD pathogen surveillance providing evidence of which viruses and bacteria are circulating, potentially informing vaccination and disease management.},
}

@article {pmid41853712,
year = {2026},
author = {Yao, J and Wang, F and Li, H and Zhang, R and Ji, G and Liu, D},
title = {Comparative analysis of microbial diversity and clinical outcomes in critically ill patients with and without malignancies: a single-center retrospective cohort study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1777861},
pmid = {41853712},
issn = {1664-302X},
abstract = {BACKGROUND: Sepsis and septic shock are severe complications for surgical malignancy patients. Conventional diagnostics often fail to capture the complex infectome in these populations. This study aimed to characterize the distinct microbial and resistome landscapes in cancer versus non-cancer patients using multi-site metagenomic next-generation sequencing (mNGS) to support specific antimicrobial strategies.

METHODS: We conducted a single-center retrospective cohort study at the General Surgery ICU of Xuanwu Hospital, including 107 septic shock patients (52 cancer; 55 non-cancer). mNGS was performed on blood, bile, ascitic fluid, and bronchoalveolar lavage samples to identify pathogens and antibiotic resistance genes (ARGs). Findings were analyzed for their association with ICU length of stay and mortality.

RESULTS: Cancer patients were significantly older (median 68 vs. 51 years, p < 0.0001) with higher comorbidity scores (CCI: 7.0 vs. 4.0, p = 0.006). However, mNGS revealed a lower pathogen detection rate in cancer patients (53.85% vs. 85.45%, p = 0.0006) and a lower incidence of bacteremia (25.0% vs. 45.45%, p = 0.0426). Cancer patients had shorter ICU LOS (9 vs. 13 days, p = 0.0369) and antibiotic durations (7 vs. 11 days, p = 0.0368). Dominant pathogens included Klebsiella pneumoniae and Enterococcus faecium, harboring diverse ARGs across beta-lactam and aminoglycoside categories. Multivariate Cox regression identified IL-6 (p = 0.018) was significant prognostic indicators for cancer patients. We also examined the distribution of virulence factors, despite their low detection rates.

CONCLUSION: Septic shock in cancer patients exhibits a unique resistome signature and distinct prognostic drivers. The identification of microbial targets via mNGS was associated with the implementation of targeted antimicrobial strategies and inflammation monitoring. These findings suggest that mNGS provides valuable molecular insights that may support clinical management and prognostic stratification for cancer patients in the surgical ICU.},
}

@article {pmid41853717,
year = {2026},
author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F},
title = {Multi-guild microbial cooperation sustains long-term anaerobic toluene degradation through sulfur cycling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1773863},
pmid = {41853717},
issn = {1664-302X},
abstract = {Anaerobic degradation of aromatic hydrocarbons such as toluene plays a critical role in the natural and engineered attenuation of contaminated environments. Here, we developed and characterized a microbial consortium enriched under strictly anoxic conditions, capable of sustained toluene degradation through sulfate reduction. By integrating biodegradation kinetics, long-read 16S rRNA profiling, and genome-resolved metagenomics, we elucidated the structure and function of a multi-guild community. The consortium was co-dominated by Desulfoprunum, a sulfate-reducing bacterium (SRB), and Sulfurovum-affiliated sulfur oxidizers (~34% each), with additional members including Stenotrophomonas, Achromobacter, and Stutzerimonas. Such co-dominance appears uncommon, as sulfate-reducing enrichments are often characterized by low diversity and the predominance of a single lineage, such as Desulfobacula or Desulfosarcina in marine systems. Genome-resolved analyses recovered seven metagenome-assembled genomes (MAGs) with distinct but complementary metabolic roles. Desulfoprunum encoded the fumarate-addition pathway (bss/bbs) for anaerobic toluene activation and dissimilatory sulfate reduction (aprAB, dsrAB). In contrast, Sulfurovum and several Gammaproteobacteria encoded sulfide:quinone oxidoreductase (sqr), coupling H2S detoxification to energy conservation, while a Moranbacterales MAG carried a putative sulfhydrogenase (hydAB) potentially catalyzing elemental sulfur (S°) reduction. Additional MAGs encoded assimilatory sulfate reduction (cys), suggesting integration of sulfur into biosynthetic pathways. Together, these features are consistent with the presence of a putative distributed sulfur redox loop, in which biogenic H2S may be recycled via oxidation and reduction reactions mediated by co-occurring taxa. This sulfur loop is hypothesized to contribute to buffering sulfide toxicity and stabilize redox dynamics, thereby potentially supporting long-term toluene degradation under sulfidic conditions. Our findings highlight anaerobic degradation as a community-driven process enabled by sulfur-cycling interactions. By revealing the role of cryptic sulfur cycling in stabilizing hydrocarbon degradation, this work offers a new framework for designing bioremediation strategies in contaminated anoxic environments.},
}

@article {pmid41853758,
year = {2025},
author = {Song, W and Liu, S and Zang, D and Meng, W and Liu, C and Chen, J},
title = {Correlation between gut microbiota and their metabolites and the efficacy of chemotherapy combined with immunotherapy for extensive-stage small cell lung cancer.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1683347},
pmid = {41853758},
issn = {2234-943X},
abstract = {INTRODUCTION: Gut microbiota has been reported to be associated with the host's immune system and immunotherapy response, as well as immune-related adverse events (irAEs). Additionally, gut microbial metabolites have various immunomodulatory effects. Our study focused on the differences in gut microbiota and their metabolites between long progression-free survival (PFS) and short PFS in patients with small cell lung cancer before and after chemotherapy combined with immunotherapy.

METHODS: The enrolled patients collected in our department were divided into long PFS and short PFS groups according to whether the PFS was ≥6 months, and the stool samples before and after treatment were analyzed using metagenomics and metabolomics.

RESULTS: The results showed that Streptococcus (P = 0.00648), Actinomyces (P = 0.0124), and Roseburia (P = 0.0127) differed between the long and short PFS groups. In the analysis of differential metabolites, we found that indirubin-3'-monoxime (AUC 0.611), stearidonic acid (AUC 0.867), leukotriene B4 (AUC 0.844), trans-cinnamic acid (AUC 0.792), and L-tyrosine (AUC 0.751) could be used as potential biomarkers.

DISCUSSION: Gut microbiota and their metabolites hold broad prospects for translational applications in cancer clinical management, such as the development of microbial biomarkers and the modulation of microbiota to enhance the efficacy of chemotherapy and immunotherapy.},
}

@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}

*Ecosystem
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Metagenome
*Lakes/microbiology
*Fresh Water/microbiology
Metagenomics
Transcriptome

@article {pmid41854100,
year = {2026},
author = {Hu, K and Qu, Q and Ban, Z and Hu, X and Wang, A and Dong, X and Liu, C and Deng, P and Wang, R},
title = {Risks of Microplastics Shaping Viral Communities and Functions in Real Marine Environments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17054},
pmid = {41854100},
issn = {1520-5851},
abstract = {Microplastic (MP) pollution has become a global issue, especially in the oceans. However, the extent of changes in the ecological states of viruses that coexist with MPs and their subsequent influence on the biogeochemical cycle remain unclear. We found that the subtropical Atlantic has emerged as a viral diversity hotspot, while the hotspots of increasing viral diversity are concentrated in the South China and Eastern Archipelagic Seas, with 87.57% of the area showing increasing trends. Ignoring the effects of MPs would result in more than 15% underestimation of viral diversity in the Mediterranean region and temperate zone of the Indian Ocean, which is notably higher than the global overall underestimation of 2.4% for viral diversity. Beyond a critical MP threshold (1 × 10[4] items·km[-2], accounting for 55.26% of marine zones during 2025), a distinct positive association with marine viral diversity was observed, especially in low-diversity regions. In regions with higher MP concentrations, viral community networks exhibited higher connectivity and lower modularity, coinciding with a stronger presence of lytic bacteriophages for lysogenization. MPs emerge as significant environmental indicators linked to marine viral ecological niches and host-virus interactions. This work addresses the non-negligible role of MPs in shaping marine ecosystems by viruses.},
}

@article {pmid41854101,
year = {2026},
author = {Liu, Q and Wu, S and Gong, S and Su, H and Jin, Y and Chen, H and Fan, Y and Yin, R and Ren, X and Wang, J},
title = {Ecologically Informed Design of Synthetic Microbial Community Enables Robust Degradation and Engraftment for Antibiotic Removal in Wastewater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01020},
pmid = {41854101},
issn = {1520-5851},
abstract = {Conventional biological wastewater treatment often fails to remove emerging contaminants (ECs) because specialized degraders are absent. We developed a function-ecology-integrated framework for designing synthetic microbial communities (SynComs) by combining metagenome-guided identification of degradation potential, quorum-sensing functionality screening, and keystone-based selection from genome-scale metabolic models (GSMMs). Applied to sulfamethoxazole (SMX) degradation, this approach identified five strains with stable catabolic potential and high ecological coherence. GSMM simulations predicted SynCom5 (three species) and SynCom11 (four species) would achieve the highest SMX uptake fluxes (30.7 and 31.7 mmol gDW[-1] h[-1], respectively), driven by complementary amino acid cross-feeding and a high ratio of metabolic interaction potential to resource overlap. Experimentally, both SynComs removed >90% of SMX within 72 h, with SynCom11 selected for bioaugmentation. In activated sludge microcosms, SynCom11 achieved 91.3% SMX removal over 7 days, compared to 25.8% in controls, and successfully engrafted 2 of its 4 members. This approach avoids high-concentration selective pressure, minimizing resistance risks, and demonstrates that embedding an ecologically informed design within catabolic function enables robust, scalable bioaugmentation for ECs.},
}

@article {pmid41854267,
year = {2026},
author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ},
title = {Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0106225},
doi = {10.1128/msystems.01062-25},
pmid = {41854267},
issn = {2379-5077},
abstract = {Metagenomes often contain many reads derived from eukaryotes, but there is usually no reliable method for estimating their prevalence. This forces many analysis techniques to make the often-faulty assumption that all reads are prokaryotic. Here, we present SingleM prokaryotic_fraction (SPF), an algorithm that scalably and robustly estimates the number of bacterial and archaeal reads in a metagenome. It also estimates the average genome size of bacteria/archaea in a sample. SPF does not use eukaryotic reference genome data and can be applied to any modern Illumina metagenome. Based on SPF, we propose the domain-adjusted mapping rate (DAMR) as an improved metric to assess prokaryotic genome recovery from metagenomes. Applying SPF to 136,284 publicly available metagenomes, we report substantial variation in prokaryotic fractions and biome-specific patterns of prokaryotic abundance, providing insights into how microorganisms and eukaryotes are distributed across Earth. Finally, we show that substantial amounts of human host DNA sequence data have been deposited in public metagenome repositories, possibly counter to ethical directives that mandate screening of these reads prior to release. As the adoption of metagenomic sequencing continues to grow, we foresee SPF being a valuable tool for the appraisal of genome recovery efforts and for investigating global patterns of microorganism distribution.IMPORTANCEMetagenomics data sets capture DNA from all organisms in a sample, enabling the analysis of communities without relying on culture-based techniques. However, many samples include uncharacterized eukaryotic organisms and viral elements, meaning the proportion of bacterial and archaeal DNA is often unknown. This study presents SingleM prokaryotic_fraction (SPF), a robust and scalable method for estimating the prevalence of bacterial and archaeal DNA in metagenomes. Crucially, SPF is calculated independent of eukaryotic and viral reference genomes, which are often incomplete or unavailable. Applying SPF to over 136,000 public metagenomes uncovered substantial variability between microbial communities living in different environments. SPF also identified previously overlooked human genetic data contamination in public data sets, raising important ethical and privacy considerations. Building on SPF, we propose the domain-adjusted mapping rate (DAMR) metric, a new metric that improves genome recovery assessment by accounting for non-prokaryotic reads.},
}

@article {pmid41854352,
year = {2026},
author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J},
title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.},
journal = {Lupus},
volume = {},
number = {},
pages = {9612033261432163},
doi = {10.1177/09612033261432163},
pmid = {41854352},
issn = {1477-0962},
abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.},
}

@article {pmid41854356,
year = {2026},
author = {Khadivar, H and Bui, H and Huesemann, M and Gao, S and Gerlach, R},
title = {Metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. PNNL-SSL1.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0139825},
doi = {10.1128/mra.01398-25},
pmid = {41854356},
issn = {2576-098X},
abstract = {Microalgae and cyanobacteria are promising sources of fuels, chemicals, and bioproducts, but CO2 supply increases production cost. We present the metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. strain PNNL-SSL1 obtained from Soap Lake (Washington, USA). PNNL-SSL1 shows strong potential for biomass production using only atmospheric CO2, reducing cultivation expenses.},
}

@article {pmid41854421,
year = {2026},
author = {Colina Prisco, C and Fourie, NH and Wang, Y and Steck, M and de Jesús Vega, M and Graves-Dixon, LY and Jaime-Lara, RB and Henderson, WA and Joseph, PV},
title = {Examining mRNA-miRNA Interactions and Gene Expression in Overweight and Obesity.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261433237},
doi = {10.1177/10998004261433237},
pmid = {41854421},
issn = {1552-4175},
abstract = {Obesity is characterized by excess adipose tissue, metabolic imbalance, and persistent low-grade inflammation, all of which can affect brain centers and their communication with peripheral organs. The genetic basis of obesity is complex, involving genetics, metagenomics, and gene-environment interactions that impact gene expression. Micro-RNAs (miRNAs) are small, single-stranded, non-coding RNAs that post-transcriptionally regulate the translational rates of target messenger RNAs (mRNAs). Exploring miRNA-mRNA interactions in obesity offers insights into molecular processes, potential biomarkers, and therapeutic targets of this condition. The current study examined the interplay between miRNA and mRNA collected from individuals with overweight and obesity, and normal weight controls. To our knowledge, this is the first experimental attempt to construct a comprehensive dataset of miRNA-mRNA interactions in overweight and obesity. Total RNA, including miRNA, was isolated from venous blood samples collected from 95 participants. Subsequently, 100 ng of RNA from each sample was analyzed using the NanoString quantitative assay. Quantile normalization, the Bayesian-based method Combat, multi-variable linear regression, over-representation, weighted gene correlation network analyses, and functional analyses were conducted. We found an association between IQGAP1 and DAZAP2 genes and miRNA-20-a and miRNA-2113. IQGAP1 and DAZAP2 were associated with insulin signaling and energy metabolism and insulin sensitivity, respectively. We also identified a positive correlation between peripheral cortisol levels and miRNA-548 with alterations in metabolic processes and the immune system. This suggests that miRNA-mRNA interactions in overweight and obesity may impact insulin sensitivity, metabolism, and immunity, providing novel insight into miRNA-mRNA interactions in overweight and obesity. (ClinicalTrials.gov identifier #NCT00824941; https://clinicaltrials.gov/study/NCT00824941).},
}

@article {pmid41854491,
year = {2026},
author = {Wang, HC and Zhang, Y and Feng, R and Cai, LT and Chen, X and Hsiang, T and Wang, F},
title = {Metagenomic Analysis of Potential Pathogens and Other Microorganisms in Tobacco Leaves.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS03250520RE},
doi = {10.1094/PDIS-03-25-0520-RE},
pmid = {41854491},
issn = {0191-2917},
abstract = {Tobacco leaf spot is a major challenge for tobacco leaf production, and the phyllosphere of tobacco is the main habitat for many pathogens. In this study, tobacco leaves with typical symptoms were sampled, and morphological and molecular biological methods were used to identify pathogens. Illumina high-throughput sequencing and Biolog-ECO were used to investigate the composition and carbon metabolic capacity of the microorganisms in the tobacco leaves. A total of 24 fungal isolates were obtained, including one taxon each of Diaporthe, Paramyrothecium, Botrytis, Phoma, and Mortierella; six each of Fusarium and Epicoccum; four of Trichoderma; and three of Alternaria. Six genera of bacteria were isolated: Bacillus, Pantoea, Enterobacter, Pseudomonas, Prolinoborus, and Atlantibacter. Pathogenicity tests revealed that four isolates of Epicoccum and three isolates of Alternaria were pathogenic, and the leaf spot symptoms induced by coinfection with members from these two groups were similar to those observed in the field. These pathogens were identified as Epicoccum latusicollum and Alternaria alternata through multigene analysis. High-throughput sequencing analysis showed that the dominant fungi in diseased tobacco tissues were Alternaria and Epicoccum, and the dominant bacteria were Pseudomonas, Paenibacillus, and Pantoea. In carbon source utilization tests, where various carbohydrates were the main carbon sources, the utilization capacity of phyllosphere microorganisms in diseased tobacco leaves was lower than that in healthy leaves. The combined application of culture-dependent and independent methods provided comprehensive insights into plant disease diagnosis and tobacco phyllosphere microorganism community composition and metabolic function.},
}

@article {pmid41854683,
year = {2026},
author = {Wang, J and Shi, Y and Jia, Y and Peng, J},
title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71679},
doi = {10.1096/fj.202503650RRR},
pmid = {41854683},
issn = {1530-6860},
support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced ; Male ; Metabolomics/methods ; Metagenomics/methods ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Metabolome/drug effects ; },
abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Flavonoids/pharmacology
Mice
*Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced
Male
Metabolomics/methods
Metagenomics/methods
Fecal Microbiota Transplantation
Mice, Inbred C57BL
*Metabolome/drug effects

@article {pmid41855720,
year = {2026},
author = {Miao, H and Zeng, W and Hao, X and Gu, Y and Peng, Y},
title = {S[0]-S[2-] co-substrate system achieves efficient nitrite accumulation under high alkalinity and ultra-short HRT: Multidimensional responses and metabolic regulation mechanism.},
journal = {Water research},
volume = {297},
number = {},
pages = {125737},
doi = {10.1016/j.watres.2026.125737},
pmid = {41855720},
issn = {1879-2448},
abstract = {Sulfur autotrophic denitrification under highly alkaline conditions provides a novel strategy for nitrite supply, but low nitrate conversion flux often limits nitrite accumulation rate. This study proposes an element sulfur-sulfide (S[0]-S[2][-]) co-substrate enhancement strategy based on an alkaline environment. Under high pH (10) with an ultra-short hydraulic retention time (0.65 h) and low S[2][-] feeding (S[2-]/NO3[-]-N ratio of 0.17), the nitrate conversion efficiency (84.3%) was nearly 20% higher than that only at high pH conditions. Moreover, the strategy achieved an excellent nitrite accumulation efficiency of 60.6% and a rate of 1.54 kg N·m[-3]· d[-1]. Microbial physiological responses revealed that reactive oxygen species accumulation significantly inhibited microbial activity and disrupted nitrogen-sulfur metabolism at high pH. However, supplemental S[2-] promoted the ring-opening activation of S[0] to form high bioavailability polysulfide, and restored electron transfer system activity and energy metabolism. The abundance of sulfur-oxidizing genes Sox and fccAB increased by 15.7%-95.6%, ensuring robust electron flux. Under this strategy, the system exhibited an optimized metabolic trade-off that prioritized survival advantages over complete denitrification. This was achieved by prioritizing energy allocation to Na[+](K[+])/H[+] antiporters (Mrp/Pha/Kef/Trk) and glutamate synthesis to maintain cellular homeostasis. Concurrently, the increased narGHI/napAB abundance (14.6%-58.9%) and reduced nirS abundance (25.6%-41.3%) ensured a higher nitrite accumulation rate. Functional annotation further revealed that Thiobacillus (40.2%) and Pseudoxanthomonas (3.9%) served as key genera driving nitrite accumulation. This study not only proposes an efficient nitrite supply strategy for Anammox but also reveals the underlying microbial response mechanisms under high alkalinity.},
}

@article {pmid41855876,
year = {2026},
author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J},
title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129409},
doi = {10.1016/j.jenvman.2026.129409},
pmid = {41855876},
issn = {1095-8630},
abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.},
}

@article {pmid41855937,
year = {2026},
author = {Jiang, L and Liang, Z and Williams, TA and Deng, Y and Yu, H and Hao, Q and Cao, J and Zhou, H and Lai, H and Chen, J and Chen, H and Zhang, C},
title = {Vertical stratification and metabolic versatility of methanogens in Haima cold seep sediments: Alkane-fueled acetoclastic methanogenesis revealed by metagenomics and experimental verification.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107972},
doi = {10.1016/j.marenvres.2026.107972},
pmid = {41855937},
issn = {1879-0291},
abstract = {Cold seeps are hot spots for studying the biogeochemical processes mediated by methyl-coenzyme M reductase (MCR) containing archaea, yet these processes remain poorly understood. Here, we investigated the microbial communities in a 5-m-long sediment core encompassing sulfate-methane transition zone (SMTZ), collected from the Haima cold seep. We focused on distinct biogeochemical characteristics and metagenomics to study the vertical patterns of mcrA-containing archaea and their role in alkane metabolism. Background alkane analysis showed that long chain alkanes were dominant in the sediment core. Metagenomic and quantitative PCR (qPCR) analysis revealed that the abundance of mcrA gene within and below the SMTZ were substantially higher than those above the SMTZ. We recovered 21 mcrA-containing MAGs, 11 affiliated with Methanosarcinaceae. One MAG (CG1-BIN56) encoded complete key genes for all three methanogenic pathways. Functional gene profiles suggested that acetoclastic methanogenesis is the dominant pathway. Furthermore, a 10-month anaerobic enrichment with n-alkanes (C10/C16) using SMTZ (CG15: 350 cmbsf) inocula exhibited high degradation rate (C10: 94.2% ± 2.5%, C16: 66.8% ± 2.8%) accompanied by acetate accumulation. These findings suggest that acetate, as a likely intermediate associated with alkane degradation process, potentially fuels acetoclastic methanogenesis. This indicates a likely syntrophic interaction between alkane-degrading and methane-cycling microorganisms in cold seep sediments.},
}

@article {pmid41855981,
year = {2026},
author = {Ye, T and Li, P and Zhou, Z and Xiong, B and Zhao, Y and Zhao, J and Qi, J and Ma, B and Chen, Y},
title = {Enhanced pollutant removal in multi-pollutants contaminated water by bioaugmented slow filtration.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141806},
doi = {10.1016/j.jhazmat.2026.141806},
pmid = {41855981},
issn = {1873-3336},
abstract = {Slow filtration is a low-cost and low-carbon water treatment approach, yet its broad application is limited by long start-up times and insufficient understanding of multi-pollutant removal. Here, we evaluate whether bioaugmentation with manganese-oxidizing bacteria enhances pollutant removal in water contaminated with NH4[+] -N, Mn[2+], readily biodegradable emerging contaminants (ECs, atenolol and trimethoprim), and relatively non-biodegradable ECs (carbamazepine and sulfamethoxazole). Bioaugmented filtration increased the removal rates of NH4[+]-N and Mn[2+] by 32.2% and 33.9%, respectively, during the first 10 days of the experiment. The proposed approach also demonstrated superior average removal rates (30.1%-99.6%) of four ECs compared to the filter column without QJX-1 inoculation (16.7%-99.3%). Furthermore, bioaugmented filtration effectively reduced the relative abundances of antibiotic resistance genes (ARGs) subtypes such as macB, tetA(58), and bcrA in the influent. The composition of ARGs on the filter media in both process groups is highly similar, with the relative abundance of ARGs at the top and middle of the filter column slightly higher than at the bottom. The mechanism study revealed that Mn[2+] was effectively oxidized to biological manganese oxides, which was conducive to the adsorption and oxidation of Mn[2+] and ECs. The metagenomic results confirmed the pmoC-amoC gene in Nitrospira promoted the removal of NH4[+]-N. Toxicity prediction indicated that the toxicity of most ECs intermediates was significantly lower than that of their parent compounds. The findings of this study verify the viability of employing cost-effective and few-chemical water treatment technologies to treat muti-pollutant contaminated water and guarantee the quality of drinking water.},
}

@article {pmid41855987,
year = {2026},
author = {Demaria, F and Suleiman, M and Bargiela, R and Ferrer, M and Hernández, SB and Núñez, AE and Petchey, OL and Corvini, PF and Junier, P},
title = {Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141801},
doi = {10.1016/j.jhazmat.2026.141801},
pmid = {41855987},
issn = {1873-3336},
abstract = {Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 µg/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation.},
}

@article {pmid41856032,
year = {2026},
author = {Caetta, A and Aasen, D and Adamcyzk, P and Yuan, H and Zhou, Y and Roberts, D and Grindle, C and Schoem, S and Hughes, A},
title = {Characterizing the microbiome of the middle ear using 16S RNA sequencing in pediatric patients with and without middle ear effusions requiring ventilation tubes.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {204},
number = {},
pages = {112798},
doi = {10.1016/j.ijporl.2026.112798},
pmid = {41856032},
issn = {1872-8464},
}

@article {pmid41856107,
year = {2026},
author = {Potloane, D and Symul, L and Ngcapu, S and Lewis, L and France, M and Vermeren, L and Elsherbini, J and Chetty, C and Mafunda, NA and Polliah, AM and Mtshali, A and Kama, A and Magini, N and Mitchev, N and Mzobe, G and Khan, A and Demidkina, BC and Goldenberg, M and Xu, J and Rutt, L and Shirtliff, B and Cook, S and Murthy, M and Hussain, F and Passmore, JS and Jaspan, HB and Kullin, B and Happel, AU and Liebenberg, L and Relman, DA and Holmes, S and Kwon, DS and Ravel, J and Mitchell, CM},
title = {VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.02.016},
pmid = {41856107},
issn = {1934-6069},
abstract = {Bacterial vaginosis (BV) is characterized by high microbial diversity. High recurrence rates following antibiotics may stem from poor recolonization by protective Lactobacillus species. This phase 1 randomized trial in the United States and South Africa evaluated two vaginally delivered live biotherapeutic products (LBPs) containing multiple Lactobacillus crispatus strains. After metronidazole treatment for BV, participants received either a placebo or 3 or 7 days of active LBPs. LBP strains were detected by metagenomics in 66.1% (47/71) of participants in the active arms in the first 5 weeks. Among those, nearly half (49%, 23/47) remained colonized at 12 weeks despite the short initial treatment course. Participants were most often colonized by one of three component strains, with no geographic differences in strain colonization observed. LBPs were safe, acceptable, and well tolerated, with no serious adverse events (AEs) reported. These results provide a foundation for the development of transformational interventions aimed at optimizing the vaginal microbiome.},
}

@article {pmid41856148,
year = {2026},
author = {Michels, EHA and Dequin, PF and Butler, JM and Guillon, A and Evrard, B and Paling, FP and Reijnders, TDY and Schuurman, AR and van Engelen, TSR and Brands, X and Haak, BW and Bos, LDJ and Leroux, C and Giamarellos-Bourboulis, EJ and Stoker, J and Prins, JM and Faber, DR and Douma, RA and Sweeney, TE and Malhotra-Kumar, S and Kluytmans, JAJW and Scicluna, BP and Cremer, OL and Matthay, M and Calfee, C and Wiersinga, WJ and Peters-Sengers, H and van der Poll, T},
title = {Quantifying immune dysregulation in pneumonia and sepsis with a parsimonious machine-learning model: a multicohort analysis across care settings and reanalysis of a hydrocortisone randomised controlled trial.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00429-1},
pmid = {41856148},
issn = {2213-2619},
abstract = {BACKGROUND: Sepsis is a dysregulated host response to infection resulting in life-threatening organ failure. Although immune dysregulation is central to the sepsis definition, immunomodulation trials enrol participants based on clinical severity, not the extent of dysregulation, which could contribute to treatment heterogeneity. A pragmatic way to quantify immune dysregulation could improve prognostication, help to evaluate treatment responses, and identify individuals most likely to benefit from immunomodulation. We aimed to construct a parsimonious machine-learning tool that defines and quantifies immune dysregulation, thereby supporting biologically informed immunomodulation.

METHODS: In this multicohort analysis and reanalysis of a randomised controlled trial, the primary objective was to derive and validate a categorical and continuous immune dysregulation score that is independent of clinical presentation or outcome. We measured 35 plasma biomarkers reflecting key host response domains in individuals with community-acquired pneumonia (CAP) across different care settings (emergency department, general ward, and intensive care unit) and disease severities using data from three independent cohorts. We applied unsupervised trajectory inference analysis to identify an immune dysregulation gradient captured as discrete immune dysregulation stages (Dysregulated Immune Profile [DIP]) and a continuous score (cDIP; 0-1). We developed two parsimonious machine-learning models to predict the DIP stages and cDIP scores based on 35 biomarkers, and validated their ability to capture immune dysregulation and predict clinical outcomes in five independent cohorts. On the basis of our hypothesis that only individuals with severe immune dysregulation benefit from immunomodulation, we carried out a post-hoc analysis of a randomised trial evaluating hydrocortisone in severe CAP (CAPE COD trial, NCT02517489), assessing treatment effects across DIP stages and the cDIP continuum, and how hydrocortisone influenced dysregulation trajectories over time.

FINDINGS: We organised 398 participants with CAP along a continuum of immune dysregulation from mild to severe on the basis of 35 plasma biomarkers, yielding three dysregulation stages (DIP1-3) and a continuous score (cDIP). Clinical severity proved to be an inadequate proxy for immune dysregulation. A three-biomarker machine-learning framework (procalcitonin, soluble TREM-1, and IL-6) accurately predicted the degree of dysregulation derived from 35 biomarkers (DIP stage accuracy 91·2%; cDIP root mean square error 0·056). Although the framework was not designed for outcome prediction, increased immune dysregulation-reflected in DIP and cDIP-was associated with a gradual rise in mortality (cDIP odds ratio [OR] 1·26 [95% CI 1·13-1·40] per 10% increase, p<0·0001) and secondary infections (OR 1·50 [1·22-1·93] per 10% increase, p=0·0005), independent of clinical severity. The three-biomarker tool was validated in five external cohorts of varying infections, severities, and care settings (n=1191). Reanalysis of the CAPE COD trial showed that hydrocortisone conferred a survival benefit only in participants classified as severely dysregulated by our model (30-day mortality: DIP3 OR 0·25 [0·05-0·85], p=0·042; cDIP ≥0·63 OR 0·21 [0·10-0·72], p=0·011), accompanied by faster immune recovery (time × treatment interaction, p<0·0001). No such effect modification was observed when stratifying participants by clinical severity.

INTERPRETATION: We have provided a publicly available three-biomarker framework to determine the extent of host response dysregulation with potential value for precision-guided immunomodulatory therapy.

FUNDING: EU Horizon 2020.},
}